Starting phenix.real_space_refine on Wed Jul 1 21:28:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j7u_61210/07_2026/9j7u_61210.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j7u_61210/07_2026/9j7u_61210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9j7u_61210/07_2026/9j7u_61210.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j7u_61210/07_2026/9j7u_61210.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j7u_61210/07_2026/9j7u_61210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j7u_61210/07_2026/9j7u_61210.map" } resolution = 3.14 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= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 12 5.16 5 C 1930 2.51 5 N 447 2.21 5 O 498 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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2889 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2823 Classifications: {'peptide': 352} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 335} Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 66 Unusual residues: {'BG6': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-1': 3, 'POV:plan-3': 2} Unresolved non-hydrogen planarities: 15 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1 POV A 402 " occ=0.75 ... (27 atoms not shown) pdb=" P POV A 402 " occ=0.75 Time building chain proxies: 0.92, per 1000 atoms: 0.32 Number of scatterers: 2889 At special positions: 0 Unit cell: (69.7, 72.25, 72.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 2 15.00 O 498 8.00 N 447 7.00 C 1930 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 245 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.28 Conformation dependent library (CDL) restraints added in 101.8 milliseconds 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 660 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 0 sheets defined 83.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 1 through 23 removed outlier: 3.518A pdb=" N MET A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 37 Processing helix chain 'A' and resid 38 through 45 removed outlier: 3.789A pdb=" N ALA A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.770A pdb=" N ILE A 49 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 80 Processing helix chain 'A' and resid 83 through 91 removed outlier: 4.748A pdb=" N LEU A 89 " --> pdb=" O TYR A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 96 removed outlier: 4.545A pdb=" N ASN A 96 " --> pdb=" O TYR A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 138 removed outlier: 3.537A pdb=" N VAL A 126 " --> pdb=" O GLY A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 173 removed outlier: 3.609A pdb=" N TRP A 160 " --> pdb=" O TRP A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 195 removed outlier: 3.563A pdb=" N VAL A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 229 removed outlier: 3.534A pdb=" N ALA A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 238 removed outlier: 3.685A pdb=" N LEU A 238 " --> pdb=" O LEU A 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 235 through 238' Processing helix chain 'A' and resid 239 through 244 removed outlier: 4.000A pdb=" N ARG A 243 " --> pdb=" O GLU A 239 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TRP A 244 " --> pdb=" O LYS A 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 239 through 244' Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.543A pdb=" N VAL A 251 " --> pdb=" O PRO A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 255 removed outlier: 3.696A pdb=" N THR A 255 " --> pdb=" O HIS A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 255' Processing helix chain 'A' and resid 256 through 276 Processing helix chain 'A' and resid 277 through 285 Processing helix chain 'A' and resid 291 through 310 removed outlier: 3.735A pdb=" N LEU A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 331 Processing helix chain 'A' and resid 331 through 339 removed outlier: 4.109A pdb=" N LEU A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 350 196 hydrogen bonds defined for protein. 582 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: 0.40 Time building geometry restraints manager: 0.32 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: 421 1.31 - 1.44: 890 1.44 - 1.56: 1647 1.56 - 1.69: 2 1.69 - 1.82: 17 Bond restraints: 2977 Sorted by residual: bond pdb=" O12 POV A 402 " pdb=" P POV A 402 " ideal model delta sigma weight residual 1.657 1.508 0.149 2.00e-02 2.50e+03 5.54e+01 bond pdb=" O6 BG6 A 401 " pdb=" P BG6 A 401 " ideal model delta sigma weight residual 1.723 1.640 0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" C31 POV A 402 " pdb=" O31 POV A 402 " ideal model delta sigma weight residual 1.327 1.396 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C21 POV A 403 " pdb=" O21 POV A 403 " ideal model delta sigma weight residual 1.330 1.399 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C21 POV A 404 " pdb=" O21 POV A 404 " ideal model delta sigma weight residual 1.330 1.398 -0.068 2.00e-02 2.50e+03 1.17e+01 ... (remaining 2972 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 3985 2.37 - 4.74: 50 4.74 - 7.11: 14 7.11 - 9.48: 5 9.48 - 11.85: 2 Bond angle restraints: 4056 Sorted by residual: angle pdb=" O13 POV A 402 " pdb=" P POV A 402 " pdb=" O14 POV A 402 " ideal model delta sigma weight residual 121.11 109.26 11.85 3.00e+00 1.11e-01 1.56e+01 angle pdb=" O11 POV A 402 " pdb=" P POV A 402 " pdb=" O12 POV A 402 " ideal model delta sigma weight residual 97.67 109.36 -11.69 3.00e+00 1.11e-01 1.52e+01 angle pdb=" C32 POV A 402 " pdb=" C31 POV A 402 " pdb=" O31 POV A 402 " ideal model delta sigma weight residual 110.66 120.10 -9.44 3.00e+00 1.11e-01 9.89e+00 angle pdb=" CA PRO A 334 " pdb=" N PRO A 334 " pdb=" CD PRO A 334 " ideal model delta sigma weight residual 112.00 107.62 4.38 1.40e+00 5.10e-01 9.78e+00 angle pdb=" O2P BG6 A 401 " pdb=" P BG6 A 401 " pdb=" O6 BG6 A 401 " ideal model delta sigma weight residual 100.73 109.82 -9.09 3.00e+00 1.11e-01 9.19e+00 ... (remaining 4051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.47: 1440 13.47 - 26.93: 189 26.93 - 40.40: 58 40.40 - 53.86: 26 53.86 - 67.33: 9 Dihedral angle restraints: 1722 sinusoidal: 695 harmonic: 1027 Sorted by residual: dihedral pdb=" CB CYS A 109 " pdb=" SG CYS A 109 " pdb=" SG CYS A 245 " pdb=" CB CYS A 245 " ideal model delta sinusoidal sigma weight residual 93.00 128.10 -35.10 1 1.00e+01 1.00e-02 1.75e+01 dihedral pdb=" CA THR A 145 " pdb=" C THR A 145 " pdb=" N TYR A 146 " pdb=" CA TYR A 146 " ideal model delta harmonic sigma weight residual 180.00 162.49 17.51 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA ASP A 25 " pdb=" CB ASP A 25 " pdb=" CG ASP A 25 " pdb=" OD1 ASP A 25 " ideal model delta sinusoidal sigma weight residual -30.00 -82.10 52.10 1 2.00e+01 2.50e-03 9.26e+00 ... (remaining 1719 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 231 0.024 - 0.048: 130 0.048 - 0.072: 59 0.072 - 0.096: 17 0.096 - 0.120: 19 Chirality restraints: 456 Sorted by residual: chirality pdb=" CA PHE A 195 " pdb=" N PHE A 195 " pdb=" C PHE A 195 " pdb=" CB PHE A 195 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.59e-01 chirality pdb=" CA PRO A 178 " pdb=" N PRO A 178 " pdb=" C PRO A 178 " pdb=" CB PRO A 178 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.11 2.00e-01 2.50e+01 3.26e-01 chirality pdb=" CA VAL A 99 " pdb=" N VAL A 99 " pdb=" C VAL A 99 " pdb=" CB VAL A 99 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.19e-01 ... (remaining 453 not shown) Planarity restraints: 487 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 333 " 0.069 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO A 334 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO A 334 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 334 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 86 " -0.017 2.00e-02 2.50e+03 1.29e-02 4.18e+00 pdb=" CG TRP A 86 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A 86 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP A 86 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 86 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 86 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 86 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 86 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 86 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 86 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 92 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.79e+00 pdb=" C ASP A 92 " 0.023 2.00e-02 2.50e+03 pdb=" O ASP A 92 " -0.009 2.00e-02 2.50e+03 pdb=" N TYR A 93 " -0.008 2.00e-02 2.50e+03 ... (remaining 484 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 151 2.73 - 3.27: 2789 3.27 - 3.82: 4691 3.82 - 4.36: 5226 4.36 - 4.90: 9643 Nonbonded interactions: 22500 Sorted by model distance: nonbonded pdb=" OD2 ASP A 69 " pdb=" ND2 ASN A 264 " model vdw 2.191 3.120 nonbonded pdb=" OE1 GLU A 110 " pdb=" O4 BG6 A 401 " model vdw 2.305 3.040 nonbonded pdb=" OH TYR A 85 " pdb=" O GLU A 110 " model vdw 2.346 3.040 nonbonded pdb=" O PRO A 144 " pdb=" OG1 THR A 145 " model vdw 2.400 3.040 nonbonded pdb=" OE2 GLU A 319 " pdb=" OH TYR A 323 " model vdw 2.435 3.040 ... (remaining 22495 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=0.75 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: 3.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.680 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.149 2978 Z= 0.283 Angle : 0.763 11.850 4058 Z= 0.323 Chirality : 0.040 0.120 456 Planarity : 0.006 0.102 487 Dihedral : 15.186 67.329 1059 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.76 (0.47), residues: 350 helix: 1.98 (0.34), residues: 266 sheet: None (None), residues: 0 loop : -1.57 (0.61), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 83 TYR 0.014 0.001 TYR A 85 PHE 0.007 0.001 PHE A 30 TRP 0.035 0.002 TRP A 86 HIS 0.002 0.001 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.28 ( 2977) covalent geometry : angle 0.76260 / 0.32 ( 4056) SS BOND : bond 0.00296 / 0.16 ( 1) SS BOND : angle 1.05585 / 0.59 ( 2) hydrogen bonds : bond 0.14162 / 10.61 ( 196) hydrogen bonds : angle 4.91185 / 4.04 ( 582) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.100 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0497 time to fit residues: 2.2748 Evaluate side-chains 28 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 ASN A 347 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.127830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.106851 restraints weight = 3814.715| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.78 r_work: 0.3136 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.0775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2978 Z= 0.145 Angle : 0.554 5.422 4058 Z= 0.284 Chirality : 0.040 0.117 456 Planarity : 0.005 0.067 487 Dihedral : 11.251 76.604 437 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.27 % Allowed : 5.19 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.68 (0.48), residues: 350 helix: 1.84 (0.33), residues: 275 sheet: None (None), residues: 0 loop : -1.68 (0.68), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 83 TYR 0.013 0.001 TYR A 127 PHE 0.013 0.001 PHE A 215 TRP 0.028 0.002 TRP A 86 HIS 0.003 0.001 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 2977) covalent geometry : angle 0.55319 / 0.28 ( 4056) SS BOND : bond 0.00202 / 0.11 ( 1) SS BOND : angle 1.09555 / 0.61 ( 2) hydrogen bonds : bond 0.05277 / 3.70 ( 196) hydrogen bonds : angle 3.98224 / 3.11 ( 582) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.140 Fit side-chains REVERT: A 276 ASN cc_start: 0.8338 (m110) cc_final: 0.8095 (m110) REVERT: A 282 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7239 (tt0) outliers start: 7 outliers final: 5 residues processed: 30 average time/residue: 0.0439 time to fit residues: 1.8525 Evaluate side-chains 31 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 347 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 0.0270 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 24 optimal weight: 0.3980 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.129284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.108242 restraints weight = 3804.985| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.78 r_work: 0.3130 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2978 Z= 0.121 Angle : 0.515 7.923 4058 Z= 0.261 Chirality : 0.039 0.116 456 Planarity : 0.005 0.049 487 Dihedral : 9.939 72.305 437 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.95 % Allowed : 8.44 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.82 (0.48), residues: 350 helix: 1.90 (0.33), residues: 277 sheet: None (None), residues: 0 loop : -1.58 (0.72), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 83 TYR 0.011 0.001 TYR A 127 PHE 0.013 0.001 PHE A 215 TRP 0.021 0.001 TRP A 86 HIS 0.002 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 2977) covalent geometry : angle 0.51458 / 0.26 ( 4056) SS BOND : bond 0.00221 / 0.12 ( 1) SS BOND : angle 0.97653 / 0.54 ( 2) hydrogen bonds : bond 0.04684 / 3.26 ( 196) hydrogen bonds : angle 3.86709 / 3.02 ( 582) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.063 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 30 average time/residue: 0.0366 time to fit residues: 1.4976 Evaluate side-chains 30 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 340 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 0.0980 chunk 15 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.128014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.106846 restraints weight = 3821.041| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.80 r_work: 0.3123 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2978 Z= 0.136 Angle : 0.518 6.603 4058 Z= 0.266 Chirality : 0.039 0.116 456 Planarity : 0.004 0.033 487 Dihedral : 9.305 68.735 437 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.95 % Allowed : 11.04 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.71 (0.48), residues: 350 helix: 1.81 (0.33), residues: 277 sheet: None (None), residues: 0 loop : -1.53 (0.72), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 83 TYR 0.013 0.001 TYR A 85 PHE 0.015 0.001 PHE A 215 TRP 0.020 0.001 TRP A 86 HIS 0.002 0.001 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 2977) covalent geometry : angle 0.51709 / 0.27 ( 4056) SS BOND : bond 0.00221 / 0.12 ( 1) SS BOND : angle 1.12419 / 0.63 ( 2) hydrogen bonds : bond 0.04823 / 3.34 ( 196) hydrogen bonds : angle 3.84618 / 2.99 ( 582) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.084 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 30 average time/residue: 0.0298 time to fit residues: 1.2459 Evaluate side-chains 29 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 291 TRP Chi-restraints excluded: chain A residue 340 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 11 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3351 r_free = 0.3351 target = 0.124869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.103564 restraints weight = 3751.863| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.78 r_work: 0.2977 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2978 Z= 0.168 Angle : 0.550 5.624 4058 Z= 0.284 Chirality : 0.041 0.116 456 Planarity : 0.004 0.034 487 Dihedral : 9.284 68.828 437 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.60 % Allowed : 11.04 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.47 (0.47), residues: 350 helix: 1.66 (0.33), residues: 276 sheet: None (None), residues: 0 loop : -1.64 (0.72), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 83 TYR 0.016 0.002 TYR A 85 PHE 0.016 0.002 PHE A 215 TRP 0.020 0.002 TRP A 86 HIS 0.003 0.001 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 ( 2977) covalent geometry : angle 0.54888 / 0.28 ( 4056) SS BOND : bond 0.00217 / 0.11 ( 1) SS BOND : angle 1.36693 / 0.77 ( 2) hydrogen bonds : bond 0.05448 / 3.76 ( 196) hydrogen bonds : angle 3.96190 / 3.07 ( 582) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.107 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 33 average time/residue: 0.0436 time to fit residues: 1.9861 Evaluate side-chains 34 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 291 TRP Chi-restraints excluded: chain A residue 340 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.126089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.104513 restraints weight = 3802.825| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.81 r_work: 0.2998 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2978 Z= 0.157 Angle : 0.545 5.350 4058 Z= 0.282 Chirality : 0.040 0.117 456 Planarity : 0.004 0.034 487 Dihedral : 9.135 68.252 437 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.92 % Allowed : 12.01 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.48), residues: 350 helix: 1.66 (0.33), residues: 277 sheet: None (None), residues: 0 loop : -1.70 (0.73), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 83 TYR 0.013 0.001 TYR A 85 PHE 0.016 0.002 PHE A 215 TRP 0.019 0.001 TRP A 86 HIS 0.003 0.001 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 2977) covalent geometry : angle 0.54475 / 0.28 ( 4056) SS BOND : bond 0.00241 / 0.13 ( 1) SS BOND : angle 1.23928 / 0.69 ( 2) hydrogen bonds : bond 0.05194 / 3.58 ( 196) hydrogen bonds : angle 3.92600 / 3.04 ( 582) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.066 Fit side-chains REVERT: A 287 LYS cc_start: 0.8495 (ptpp) cc_final: 0.7890 (mptt) REVERT: A 347 GLN cc_start: 0.7271 (OUTLIER) cc_final: 0.6132 (mt0) outliers start: 9 outliers final: 8 residues processed: 34 average time/residue: 0.0267 time to fit residues: 1.2532 Evaluate side-chains 35 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 291 TRP Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 347 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 5 optimal weight: 0.9980 chunk 9 optimal weight: 0.0020 chunk 15 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 chunk 18 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 overall best weight: 0.5188 ------------------------------------------------------------------------------- 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 = 0.3390 r_free = 0.3390 target = 0.127846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.106248 restraints weight = 3791.957| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.81 r_work: 0.3011 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2978 Z= 0.130 Angle : 0.535 8.823 4058 Z= 0.274 Chirality : 0.039 0.118 456 Planarity : 0.004 0.033 487 Dihedral : 8.887 66.395 437 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.27 % Allowed : 13.64 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.68 (0.48), residues: 350 helix: 1.82 (0.33), residues: 277 sheet: None (None), residues: 0 loop : -1.68 (0.73), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 83 TYR 0.011 0.001 TYR A 146 PHE 0.015 0.001 PHE A 215 TRP 0.019 0.001 TRP A 86 HIS 0.002 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 2977) covalent geometry : angle 0.53510 / 0.27 ( 4056) SS BOND : bond 0.00246 / 0.13 ( 1) SS BOND : angle 1.02757 / 0.56 ( 2) hydrogen bonds : bond 0.04737 / 3.27 ( 196) hydrogen bonds : angle 3.83896 / 2.97 ( 582) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.100 Fit side-chains REVERT: A 254 ASP cc_start: 0.8750 (m-30) cc_final: 0.8507 (m-30) REVERT: A 279 MET cc_start: 0.8139 (mtm) cc_final: 0.7832 (ptp) REVERT: A 287 LYS cc_start: 0.8455 (ptpp) cc_final: 0.7871 (mptt) REVERT: A 347 GLN cc_start: 0.7283 (OUTLIER) cc_final: 0.6124 (mt0) outliers start: 7 outliers final: 6 residues processed: 33 average time/residue: 0.0414 time to fit residues: 1.8932 Evaluate side-chains 34 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 291 TRP Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 347 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 23 optimal weight: 0.0980 chunk 14 optimal weight: 0.3980 chunk 3 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3394 r_free = 0.3394 target = 0.128315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.106571 restraints weight = 3839.473| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.82 r_work: 0.3029 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2978 Z= 0.123 Angle : 0.521 8.582 4058 Z= 0.265 Chirality : 0.039 0.116 456 Planarity : 0.004 0.033 487 Dihedral : 8.442 63.049 437 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.95 % Allowed : 13.96 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.79 (0.48), residues: 350 helix: 1.89 (0.33), residues: 277 sheet: None (None), residues: 0 loop : -1.64 (0.74), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 83 TYR 0.010 0.001 TYR A 146 PHE 0.016 0.001 PHE A 215 TRP 0.018 0.001 TRP A 86 HIS 0.002 0.000 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 2977) covalent geometry : angle 0.52114 / 0.26 ( 4056) SS BOND : bond 0.00252 / 0.13 ( 1) SS BOND : angle 0.97765 / 0.54 ( 2) hydrogen bonds : bond 0.04491 / 3.11 ( 196) hydrogen bonds : angle 3.77662 / 2.92 ( 582) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.064 Fit side-chains REVERT: A 254 ASP cc_start: 0.8758 (m-30) cc_final: 0.8508 (m-30) REVERT: A 287 LYS cc_start: 0.8454 (ptpp) cc_final: 0.7872 (mptt) REVERT: A 347 GLN cc_start: 0.7249 (OUTLIER) cc_final: 0.6058 (mt0) outliers start: 6 outliers final: 4 residues processed: 35 average time/residue: 0.0264 time to fit residues: 1.2895 Evaluate side-chains 33 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 291 TRP Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 347 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 17 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 9 optimal weight: 0.1980 chunk 26 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 31 optimal weight: 0.0040 chunk 30 optimal weight: 0.5980 overall best weight: 0.4392 ------------------------------------------------------------------------------- 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 = 0.3414 r_free = 0.3414 target = 0.129709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.107887 restraints weight = 3892.767| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.85 r_work: 0.3026 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2978 Z= 0.118 Angle : 0.518 8.460 4058 Z= 0.262 Chirality : 0.038 0.116 456 Planarity : 0.004 0.032 487 Dihedral : 7.707 60.162 437 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.95 % Allowed : 13.96 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.86 (0.48), residues: 350 helix: 1.95 (0.33), residues: 278 sheet: None (None), residues: 0 loop : -1.71 (0.75), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 83 TYR 0.011 0.001 TYR A 146 PHE 0.015 0.001 PHE A 215 TRP 0.018 0.001 TRP A 86 HIS 0.002 0.000 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 2977) covalent geometry : angle 0.51726 / 0.26 ( 4056) SS BOND : bond 0.00244 / 0.13 ( 1) SS BOND : angle 0.92675 / 0.51 ( 2) hydrogen bonds : bond 0.04326 / 2.99 ( 196) hydrogen bonds : angle 3.72810 / 2.88 ( 582) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.098 Fit side-chains REVERT: A 254 ASP cc_start: 0.8746 (m-30) cc_final: 0.8503 (m-30) REVERT: A 287 LYS cc_start: 0.8469 (ptpp) cc_final: 0.7861 (mptt) REVERT: A 347 GLN cc_start: 0.7248 (OUTLIER) cc_final: 0.6059 (mt0) outliers start: 6 outliers final: 5 residues processed: 32 average time/residue: 0.0382 time to fit residues: 1.7118 Evaluate side-chains 34 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 291 TRP Chi-restraints excluded: chain A residue 347 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 3 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 0.0470 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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 = 0.3507 r_free = 0.3507 target = 0.136717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.115851 restraints weight = 3795.621| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.75 r_work: 0.3025 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2905 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2978 Z= 0.122 Angle : 0.518 8.362 4058 Z= 0.263 Chirality : 0.039 0.116 456 Planarity : 0.004 0.032 487 Dihedral : 7.282 59.545 437 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.62 % Allowed : 14.29 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.90 (0.48), residues: 350 helix: 1.99 (0.33), residues: 277 sheet: None (None), residues: 0 loop : -1.70 (0.74), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 83 TYR 0.010 0.001 TYR A 85 PHE 0.015 0.001 PHE A 215 TRP 0.017 0.001 TRP A 86 HIS 0.002 0.000 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 2977) covalent geometry : angle 0.51746 / 0.26 ( 4056) SS BOND : bond 0.00239 / 0.13 ( 1) SS BOND : angle 0.98537 / 0.54 ( 2) hydrogen bonds : bond 0.04408 / 3.04 ( 196) hydrogen bonds : angle 3.73717 / 2.89 ( 582) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.105 Fit side-chains REVERT: A 208 LYS cc_start: 0.7150 (mmmt) cc_final: 0.6716 (ttmt) REVERT: A 254 ASP cc_start: 0.8767 (m-30) cc_final: 0.8533 (m-30) REVERT: A 287 LYS cc_start: 0.8455 (ptpp) cc_final: 0.7865 (mptt) REVERT: A 347 GLN cc_start: 0.7310 (OUTLIER) cc_final: 0.6106 (mt0) outliers start: 5 outliers final: 4 residues processed: 32 average time/residue: 0.0484 time to fit residues: 2.0652 Evaluate side-chains 34 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 291 TRP Chi-restraints excluded: chain A residue 347 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 32 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 28 optimal weight: 0.0670 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 0.0000 chunk 8 optimal weight: 0.0010 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 overall best weight: 0.2928 ------------------------------------------------------------------------------- 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 = 0.3444 r_free = 0.3444 target = 0.132174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.110393 restraints weight = 3771.243| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.82 r_work: 0.3045 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 2978 Z= 0.106 Angle : 0.500 8.430 4058 Z= 0.253 Chirality : 0.038 0.116 456 Planarity : 0.004 0.032 487 Dihedral : 6.834 58.631 437 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.27 % Allowed : 13.64 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.16 (0.48), residues: 350 helix: 2.15 (0.33), residues: 278 sheet: None (None), residues: 0 loop : -1.57 (0.76), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 83 TYR 0.011 0.001 TYR A 146 PHE 0.016 0.001 PHE A 215 TRP 0.017 0.001 TRP A 86 HIS 0.002 0.000 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 ( 2977) covalent geometry : angle 0.49984 / 0.25 ( 4056) SS BOND : bond 0.00254 / 0.13 ( 1) SS BOND : angle 0.75939 / 0.41 ( 2) hydrogen bonds : bond 0.03854 / 2.67 ( 196) hydrogen bonds : angle 3.63798 / 2.82 ( 582) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 823.62 seconds wall clock time: 14 minutes 44.66 seconds (884.66 seconds total)