Starting phenix.real_space_refine on Tue Aug 4 13:17:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/12oz_76656/08_2026/12oz_76656.cif Found real_map, /net/cci-nas-00/data/ceres_data/12oz_76656/08_2026/12oz_76656.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/12oz_76656/08_2026/12oz_76656.map" default_real_map = "/net/cci-nas-00/data/ceres_data/12oz_76656/08_2026/12oz_76656.map" model { file = "/net/cci-nas-00/data/ceres_data/12oz_76656/08_2026/12oz_76656.cif" } default_model = "/net/cci-nas-00/data/ceres_data/12oz_76656/08_2026/12oz_76656.cif" } resolution = 3.3 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= 0.003 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 24 5.16 5 C 2038 2.51 5 N 541 2.21 5 O 577 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3180 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2213 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 285, 2201 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 270} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 285, 2201 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 270} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 2237 Chain: "B" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 967 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR A 201 " occ=0.53 ... (22 atoms not shown) pdb=" OH BTYR A 201 " occ=0.47 Time building chain proxies: 1.26, per 1000 atoms: 0.40 Number of scatterers: 3180 At special positions: 0 Unit cell: (74.048, 69.056, 102.336, 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 24 16.00 O 577 8.00 N 541 7.00 C 2038 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 98 " 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: 0.24 Conformation dependent library (CDL) restraints added in 177.8 milliseconds 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 746 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 4 sheets defined 53.9% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 2 through 31 Proline residue: A 20 - end of helix Processing helix chain 'A' and resid 53 through 65 Processing helix chain 'A' and resid 73 through 99 Processing helix chain 'A' and resid 117 through 150 Proline residue: A 140 - end of helix Processing helix chain 'A' and resid 150 through 155 removed outlier: 4.475A pdb=" N GLY A 154 " --> pdb=" O VAL A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 181 through 210 removed outlier: 3.688A pdb=" N ARG A 185 " --> pdb=" O GLY A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 248 Proline residue: A 237 - end of helix Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.877A pdb=" N SER B 32 " --> pdb=" O GLY B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 108 through 114 Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 41 Processing sheet with id=AA2, first strand: chain 'B' and resid 8 through 10 Processing sheet with id=AA3, first strand: chain 'B' and resid 60 through 62 removed outlier: 6.617A pdb=" N TRP B 39 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA B 53 " --> pdb=" O MET B 37 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N MET B 37 " --> pdb=" O ALA B 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 62 removed outlier: 6.617A pdb=" N TRP B 39 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA B 53 " --> pdb=" O MET B 37 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N MET B 37 " --> pdb=" O ALA B 53 " (cutoff:3.500A) 215 hydrogen bonds defined for protein. 577 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: 0.45 Time building geometry restraints manager: 0.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1016 1.34 - 1.46: 793 1.46 - 1.58: 1414 1.58 - 1.69: 0 1.69 - 1.81: 34 Bond restraints: 3257 Sorted by residual: bond pdb=" CB VAL B 51 " pdb=" CG2 VAL B 51 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 4.67e-01 bond pdb=" CB TRP B 39 " pdb=" CG TRP B 39 " ideal model delta sigma weight residual 1.498 1.479 0.019 3.10e-02 1.04e+03 3.88e-01 bond pdb=" CB MET A 128 " pdb=" CG MET A 128 " ideal model delta sigma weight residual 1.520 1.505 0.015 3.00e-02 1.11e+03 2.59e-01 bond pdb=" CB VAL A 26 " pdb=" CG1 VAL A 26 " ideal model delta sigma weight residual 1.521 1.505 0.016 3.30e-02 9.18e+02 2.48e-01 bond pdb=" C VAL A 217 " pdb=" N PRO A 218 " ideal model delta sigma weight residual 1.335 1.342 -0.007 1.36e-02 5.41e+03 2.46e-01 ... (remaining 3252 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 4328 1.17 - 2.33: 69 2.33 - 3.50: 16 3.50 - 4.67: 2 4.67 - 5.83: 7 Bond angle restraints: 4422 Sorted by residual: angle pdb=" C LYS B 78 " pdb=" N ASN B 79 " pdb=" CA ASN B 79 " ideal model delta sigma weight residual 122.46 125.00 -2.54 1.41e+00 5.03e-01 3.24e+00 angle pdb=" CA LEU A 17 " pdb=" CB LEU A 17 " pdb=" CG LEU A 17 " ideal model delta sigma weight residual 116.30 122.13 -5.83 3.50e+00 8.16e-02 2.78e+00 angle pdb=" CA LEU A 9 " pdb=" CB LEU A 9 " pdb=" CG LEU A 9 " ideal model delta sigma weight residual 116.30 121.92 -5.62 3.50e+00 8.16e-02 2.58e+00 angle pdb=" N ASN A 248 " pdb=" CA ASN A 248 " pdb=" C ASN A 248 " ideal model delta sigma weight residual 110.28 112.20 -1.92 1.48e+00 4.57e-01 1.69e+00 angle pdb=" CA SER A 280 " pdb=" C SER A 280 " pdb=" N ARG A 281 " ideal model delta sigma weight residual 115.05 117.26 -2.21 1.74e+00 3.30e-01 1.61e+00 ... (remaining 4417 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 1824 17.06 - 34.11: 84 34.11 - 51.16: 9 51.16 - 68.22: 1 68.22 - 85.27: 1 Dihedral angle restraints: 1919 sinusoidal: 742 harmonic: 1177 Sorted by residual: dihedral pdb=" N LYS A 122 " pdb=" CA LYS A 122 " pdb=" CB LYS A 122 " pdb=" CG LYS A 122 " ideal model delta sinusoidal sigma weight residual -60.00 -114.05 54.05 3 1.50e+01 4.44e-03 9.25e+00 dihedral pdb=" N ASN A 249 " pdb=" CA ASN A 249 " pdb=" CB ASN A 249 " pdb=" CG ASN A 249 " ideal model delta sinusoidal sigma weight residual -60.00 -110.21 50.21 3 1.50e+01 4.44e-03 8.87e+00 dihedral pdb=" N LEU A 74 " pdb=" CA LEU A 74 " pdb=" CB LEU A 74 " pdb=" CG LEU A 74 " ideal model delta sinusoidal sigma weight residual -60.00 -105.02 45.02 3 1.50e+01 4.44e-03 8.10e+00 ... (remaining 1916 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.023: 261 0.023 - 0.046: 140 0.046 - 0.068: 58 0.068 - 0.091: 16 0.091 - 0.113: 17 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA VAL B 95 " pdb=" N VAL B 95 " pdb=" C VAL B 95 " pdb=" CB VAL B 95 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.19e-01 chirality pdb=" CA PRO A 237 " pdb=" N PRO A 237 " pdb=" C PRO A 237 " pdb=" CB PRO A 237 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.01e-01 chirality pdb=" CA ILE A 39 " pdb=" N ILE A 39 " pdb=" C ILE A 39 " pdb=" CB ILE A 39 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.81e-01 ... (remaining 489 not shown) Planarity restraints: 562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 236 " -0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO A 237 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 237 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 237 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 125 " 0.017 5.00e-02 4.00e+02 2.55e-02 1.04e+00 pdb=" N PRO B 126 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO B 126 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 126 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 89 " 0.015 5.00e-02 4.00e+02 2.33e-02 8.72e-01 pdb=" N PRO B 90 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO B 90 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 90 " 0.013 5.00e-02 4.00e+02 ... (remaining 559 not shown) Histogram of nonbonded interaction distances: 2.64 - 3.09: 2308 3.09 - 3.54: 3491 3.54 - 4.00: 4627 4.00 - 4.45: 5755 4.45 - 4.90: 8749 Nonbonded interactions: 24930 Sorted by model distance: nonbonded pdb=" N ASP A 216 " pdb=" O ASP A 216 " model vdw 2.639 2.496 nonbonded pdb=" N ALA B 94 " pdb=" O ALA B 94 " model vdw 2.653 2.496 nonbonded pdb=" N ASP A 299 " pdb=" O ASP A 299 " model vdw 2.654 2.496 nonbonded pdb=" N VAL A 48 " pdb=" O VAL A 48 " model vdw 2.657 2.496 nonbonded pdb=" N ALA B 52 " pdb=" O ALA B 52 " model vdw 2.659 2.496 ... (remaining 24925 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.47 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: 10.810 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.320 Find NCS groups from input model: 0.010 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:0.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3258 Z= 0.113 Angle : 0.449 5.833 4424 Z= 0.222 Chirality : 0.036 0.113 492 Planarity : 0.003 0.030 562 Dihedral : 9.323 85.275 1170 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.58 % Allowed : 3.79 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.73 (0.43), residues: 407 helix: 3.12 (0.36), residues: 199 sheet: 1.05 (0.81), residues: 42 loop : 0.43 (0.50), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 5 TYR 0.011 0.001 TYR A 23 PHE 0.009 0.001 PHE A 71 TRP 0.005 0.001 TRP A 270 HIS 0.002 0.000 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 3257) covalent geometry : angle 0.44886 / 0.22 ( 4422) SS BOND : bond 0.00183 / 0.10 ( 1) SS BOND : angle 0.82394 / 0.55 ( 2) hydrogen bonds : bond 0.14481 / 10.44 ( 202) hydrogen bonds : angle 6.06741 / 4.87 ( 577) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.071 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.9364 (mp) cc_final: 0.9134 (tp) REVERT: A 90 LYS cc_start: 0.8977 (tptt) cc_final: 0.8580 (tptt) REVERT: A 119 HIS cc_start: 0.8806 (t70) cc_final: 0.8206 (t70) REVERT: A 123 GLU cc_start: 0.9494 (pt0) cc_final: 0.9069 (pt0) REVERT: A 127 GLU cc_start: 0.9529 (mm-30) cc_final: 0.9095 (tp30) REVERT: A 205 GLU cc_start: 0.8541 (mm-30) cc_final: 0.7843 (tm-30) REVERT: A 285 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7332 (pp) REVERT: B 15 VAL cc_start: 0.9393 (t) cc_final: 0.9032 (m) REVERT: B 78 LYS cc_start: 0.9544 (mttt) cc_final: 0.9252 (mtmm) REVERT: B 79 ASN cc_start: 0.8371 (p0) cc_final: 0.8109 (p0) outliers start: 2 outliers final: 1 residues processed: 56 average time/residue: 0.0725 time to fit residues: 4.7136 Evaluate side-chains 39 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 285 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.4980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.3980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.4980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3684 r_free = 0.3684 target = 0.086718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.060687 restraints weight = 34027.666| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 8.63 r_work: 0.2763 rms_B_bonded: 7.38 restraints_weight: 2.0000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2771 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3258 Z= 0.156 Angle : 0.566 7.447 4424 Z= 0.285 Chirality : 0.038 0.139 492 Planarity : 0.004 0.031 562 Dihedral : 3.449 26.216 457 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.75 % Allowed : 7.87 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.91 (0.43), residues: 407 helix: 3.16 (0.36), residues: 201 sheet: 1.16 (0.78), residues: 42 loop : 0.62 (0.54), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 30 TYR 0.023 0.001 TYR A 296 PHE 0.015 0.001 PHE B 50 TRP 0.009 0.001 TRP A 270 HIS 0.002 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 ( 3257) covalent geometry : angle 0.56608 / 0.28 ( 4422) SS BOND : bond 0.00112 / 0.06 ( 1) SS BOND : angle 0.29381 / 0.20 ( 2) hydrogen bonds : bond 0.03842 / 2.67 ( 202) hydrogen bonds : angle 4.45413 / 3.45 ( 577) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.9479 (mp) cc_final: 0.9099 (tp) REVERT: A 90 LYS cc_start: 0.8994 (tptt) cc_final: 0.8566 (tptt) REVERT: A 119 HIS cc_start: 0.8700 (t70) cc_final: 0.7865 (t70) REVERT: A 123 GLU cc_start: 0.9239 (pt0) cc_final: 0.8635 (pt0) REVERT: A 127 GLU cc_start: 0.9414 (mm-30) cc_final: 0.9053 (tp30) REVERT: A 205 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8247 (tm-30) REVERT: A 285 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7509 (pp) outliers start: 6 outliers final: 4 residues processed: 43 average time/residue: 0.0780 time to fit residues: 4.1057 Evaluate side-chains 42 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 285 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 8.9990 chunk 33 optimal weight: 0.0770 chunk 17 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 0.3980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.087158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.058064 restraints weight = 30184.770| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 5.87 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3258 Z= 0.147 Angle : 0.536 7.057 4424 Z= 0.269 Chirality : 0.038 0.143 492 Planarity : 0.004 0.031 562 Dihedral : 3.511 26.156 457 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.62 % Allowed : 7.58 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.83 (0.43), residues: 407 helix: 3.18 (0.35), residues: 201 sheet: 1.07 (0.79), residues: 42 loop : 0.47 (0.53), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 5 TYR 0.014 0.001 TYR A 23 PHE 0.013 0.001 PHE B 50 TRP 0.008 0.001 TRP A 270 HIS 0.001 0.000 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 3257) covalent geometry : angle 0.53596 / 0.27 ( 4422) SS BOND : bond 0.00111 / 0.06 ( 1) SS BOND : angle 0.32534 / 0.22 ( 2) hydrogen bonds : bond 0.03426 / 2.39 ( 202) hydrogen bonds : angle 4.19953 / 3.23 ( 577) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.120 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.9436 (mp) cc_final: 0.9068 (tp) REVERT: A 90 LYS cc_start: 0.8983 (tptt) cc_final: 0.8588 (tptt) REVERT: A 119 HIS cc_start: 0.8572 (t70) cc_final: 0.7678 (t70) REVERT: A 123 GLU cc_start: 0.8993 (pt0) cc_final: 0.8369 (pt0) REVERT: A 127 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8856 (tp30) REVERT: A 205 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8164 (tm-30) REVERT: A 285 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7791 (pp) outliers start: 9 outliers final: 6 residues processed: 43 average time/residue: 0.0726 time to fit residues: 3.8528 Evaluate side-chains 43 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 285 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 15 optimal weight: 0.0870 chunk 21 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 27 optimal weight: 0.0970 chunk 17 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 0.0170 overall best weight: 0.2994 ------------------------------------------------------------------------------- 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 = 0.3710 r_free = 0.3710 target = 0.087891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.059605 restraints weight = 22110.335| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 5.06 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3258 Z= 0.113 Angle : 0.527 7.242 4424 Z= 0.263 Chirality : 0.038 0.147 492 Planarity : 0.004 0.031 562 Dihedral : 3.529 26.401 457 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.75 % Allowed : 8.45 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.86 (0.43), residues: 407 helix: 3.31 (0.36), residues: 195 sheet: 1.02 (0.76), residues: 42 loop : 0.47 (0.50), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 30 TYR 0.013 0.001 TYR A 23 PHE 0.009 0.001 PHE A 71 TRP 0.007 0.001 TRP A 270 HIS 0.001 0.000 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 3257) covalent geometry : angle 0.52709 / 0.26 ( 4422) SS BOND : bond 0.00053 / 0.03 ( 1) SS BOND : angle 0.27320 / 0.18 ( 2) hydrogen bonds : bond 0.03130 / 2.18 ( 202) hydrogen bonds : angle 4.02160 / 3.09 ( 577) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.118 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.9399 (mp) cc_final: 0.9017 (tp) REVERT: A 90 LYS cc_start: 0.8989 (tptt) cc_final: 0.8581 (tptt) REVERT: A 119 HIS cc_start: 0.8511 (t70) cc_final: 0.7609 (t70) REVERT: A 123 GLU cc_start: 0.8926 (pt0) cc_final: 0.8302 (pt0) REVERT: A 127 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8796 (tp30) REVERT: A 205 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8204 (tm-30) REVERT: A 285 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7691 (pp) outliers start: 6 outliers final: 3 residues processed: 43 average time/residue: 0.0746 time to fit residues: 3.9342 Evaluate side-chains 41 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 285 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 0.4980 chunk 3 optimal weight: 0.0970 chunk 2 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 24 optimal weight: 0.1980 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.087607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.060534 restraints weight = 29493.314| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 7.16 r_work: 0.2802 rms_B_bonded: 6.81 restraints_weight: 2.0000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2806 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3258 Z= 0.129 Angle : 0.552 7.534 4424 Z= 0.274 Chirality : 0.038 0.162 492 Planarity : 0.004 0.031 562 Dihedral : 3.543 26.074 457 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.33 % Allowed : 9.04 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.89 (0.42), residues: 407 helix: 3.36 (0.35), residues: 189 sheet: 1.00 (0.76), residues: 42 loop : 0.59 (0.49), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 77 TYR 0.014 0.001 TYR A 23 PHE 0.011 0.001 PHE B 50 TRP 0.007 0.001 TRP A 270 HIS 0.001 0.000 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 3257) covalent geometry : angle 0.55210 / 0.27 ( 4422) SS BOND : bond 0.00087 / 0.05 ( 1) SS BOND : angle 0.21275 / 0.14 ( 2) hydrogen bonds : bond 0.03078 / 2.15 ( 202) hydrogen bonds : angle 4.06311 / 3.13 ( 577) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.124 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.9456 (mp) cc_final: 0.9069 (tp) REVERT: A 90 LYS cc_start: 0.8987 (tptt) cc_final: 0.8569 (tptt) REVERT: A 119 HIS cc_start: 0.8694 (t70) cc_final: 0.7875 (t70) REVERT: A 123 GLU cc_start: 0.9198 (pt0) cc_final: 0.8602 (pt0) REVERT: A 127 GLU cc_start: 0.9366 (mm-30) cc_final: 0.9092 (tp30) REVERT: A 205 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8274 (tm-30) REVERT: A 285 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7467 (pp) outliers start: 8 outliers final: 5 residues processed: 44 average time/residue: 0.0773 time to fit residues: 4.1407 Evaluate side-chains 42 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 285 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 14 optimal weight: 0.0370 chunk 32 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.087065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.060052 restraints weight = 29357.873| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 7.46 r_work: 0.2775 rms_B_bonded: 6.90 restraints_weight: 2.0000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3258 Z= 0.160 Angle : 0.562 7.759 4424 Z= 0.281 Chirality : 0.039 0.171 492 Planarity : 0.004 0.031 562 Dihedral : 3.591 25.581 457 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.04 % Allowed : 9.91 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.84 (0.42), residues: 407 helix: 3.32 (0.36), residues: 189 sheet: 0.91 (0.75), residues: 42 loop : 0.57 (0.49), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 5 TYR 0.014 0.001 TYR A 23 PHE 0.015 0.001 PHE B 50 TRP 0.007 0.001 TRP A 270 HIS 0.002 0.000 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 3257) covalent geometry : angle 0.56236 / 0.28 ( 4422) SS BOND : bond 0.00132 / 0.07 ( 1) SS BOND : angle 0.19756 / 0.13 ( 2) hydrogen bonds : bond 0.03105 / 2.15 ( 202) hydrogen bonds : angle 4.06325 / 3.12 ( 577) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.9468 (mp) cc_final: 0.9100 (tp) REVERT: A 90 LYS cc_start: 0.8998 (tptt) cc_final: 0.8589 (tptt) REVERT: A 119 HIS cc_start: 0.8723 (t70) cc_final: 0.7925 (t70) REVERT: A 123 GLU cc_start: 0.9196 (pt0) cc_final: 0.8608 (pt0) REVERT: A 127 GLU cc_start: 0.9367 (mm-30) cc_final: 0.9102 (tp30) REVERT: A 205 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8284 (tm-30) REVERT: A 285 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7489 (pp) outliers start: 7 outliers final: 6 residues processed: 44 average time/residue: 0.0801 time to fit residues: 4.2881 Evaluate side-chains 43 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 109 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 33 optimal weight: 0.4980 chunk 6 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3690 r_free = 0.3690 target = 0.086801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.060045 restraints weight = 27156.140| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 6.95 r_work: 0.2795 rms_B_bonded: 6.56 restraints_weight: 2.0000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3258 Z= 0.170 Angle : 0.569 7.951 4424 Z= 0.284 Chirality : 0.039 0.176 492 Planarity : 0.004 0.032 562 Dihedral : 3.647 25.571 457 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.04 % Allowed : 9.33 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.82 (0.42), residues: 407 helix: 3.32 (0.36), residues: 189 sheet: 0.86 (0.75), residues: 42 loop : 0.55 (0.49), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 22 TYR 0.013 0.001 TYR A 23 PHE 0.014 0.001 PHE B 50 TRP 0.008 0.001 TRP A 270 HIS 0.002 0.000 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 ( 3257) covalent geometry : angle 0.56909 / 0.28 ( 4422) SS BOND : bond 0.00118 / 0.06 ( 1) SS BOND : angle 0.23586 / 0.16 ( 2) hydrogen bonds : bond 0.03082 / 2.13 ( 202) hydrogen bonds : angle 4.06754 / 3.12 ( 577) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.139 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.9459 (mp) cc_final: 0.9078 (tp) REVERT: A 90 LYS cc_start: 0.8988 (tptt) cc_final: 0.8563 (tptt) REVERT: A 119 HIS cc_start: 0.8675 (t70) cc_final: 0.7863 (t70) REVERT: A 123 GLU cc_start: 0.9155 (pt0) cc_final: 0.8565 (pt0) REVERT: A 127 GLU cc_start: 0.9291 (mm-30) cc_final: 0.9045 (tp30) REVERT: A 205 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8339 (tm-30) REVERT: A 285 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7477 (pp) REVERT: A 296 TYR cc_start: 0.6569 (p90) cc_final: 0.6251 (p90) outliers start: 7 outliers final: 6 residues processed: 41 average time/residue: 0.0576 time to fit residues: 3.0545 Evaluate side-chains 42 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 109 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 0.0020 chunk 12 optimal weight: 0.4980 chunk 22 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 6 optimal weight: 0.0060 overall best weight: 0.3404 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.087658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.060533 restraints weight = 27568.231| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 6.91 r_work: 0.2816 rms_B_bonded: 6.60 restraints_weight: 2.0000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3258 Z= 0.121 Angle : 0.558 8.063 4424 Z= 0.276 Chirality : 0.039 0.172 492 Planarity : 0.004 0.033 562 Dihedral : 3.630 26.021 457 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.46 % Allowed : 10.50 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.87 (0.42), residues: 407 helix: 3.36 (0.36), residues: 189 sheet: 0.98 (0.76), residues: 42 loop : 0.55 (0.49), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 22 TYR 0.013 0.001 TYR A 23 PHE 0.008 0.001 PHE A 71 TRP 0.006 0.001 TRP A 270 HIS 0.001 0.000 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 3257) covalent geometry : angle 0.55841 / 0.28 ( 4422) SS BOND : bond 0.00069 / 0.04 ( 1) SS BOND : angle 0.23456 / 0.16 ( 2) hydrogen bonds : bond 0.02903 / 2.01 ( 202) hydrogen bonds : angle 3.99395 / 3.09 ( 577) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.9441 (mp) cc_final: 0.9040 (tt) REVERT: A 90 LYS cc_start: 0.8977 (tptt) cc_final: 0.8556 (tptt) REVERT: A 119 HIS cc_start: 0.8703 (t70) cc_final: 0.7888 (t70) REVERT: A 123 GLU cc_start: 0.9169 (pt0) cc_final: 0.8581 (pt0) REVERT: A 127 GLU cc_start: 0.9325 (mm-30) cc_final: 0.9056 (tp30) REVERT: A 205 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8268 (tm-30) outliers start: 5 outliers final: 4 residues processed: 40 average time/residue: 0.0600 time to fit residues: 3.1015 Evaluate side-chains 38 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain B residue 109 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 35 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.086888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.057282 restraints weight = 41939.319| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 6.59 r_work: 0.2809 rms_B_bonded: 6.25 restraints_weight: 2.0000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3258 Z= 0.179 Angle : 0.578 8.207 4424 Z= 0.286 Chirality : 0.039 0.175 492 Planarity : 0.004 0.032 562 Dihedral : 3.377 19.289 455 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.17 % Allowed : 10.20 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.85 (0.42), residues: 407 helix: 3.35 (0.36), residues: 189 sheet: 0.99 (0.76), residues: 42 loop : 0.52 (0.49), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 22 TYR 0.013 0.001 TYR A 23 PHE 0.013 0.001 PHE B 50 TRP 0.009 0.001 TRP A 270 HIS 0.002 0.000 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 ( 3257) covalent geometry : angle 0.57836 / 0.29 ( 4422) SS BOND : bond 0.00140 / 0.07 ( 1) SS BOND : angle 0.17448 / 0.12 ( 2) hydrogen bonds : bond 0.02923 / 1.99 ( 202) hydrogen bonds : angle 4.02115 / 3.10 ( 577) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.122 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.9460 (mp) cc_final: 0.9081 (tp) REVERT: A 90 LYS cc_start: 0.8981 (tptt) cc_final: 0.8558 (tptt) REVERT: A 119 HIS cc_start: 0.8724 (t70) cc_final: 0.7911 (t70) REVERT: A 123 GLU cc_start: 0.9166 (pt0) cc_final: 0.8576 (pt0) REVERT: A 127 GLU cc_start: 0.9332 (mm-30) cc_final: 0.9063 (tp30) REVERT: A 205 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8270 (tm-30) REVERT: A 296 TYR cc_start: 0.6535 (p90) cc_final: 0.6214 (p90) outliers start: 4 outliers final: 4 residues processed: 39 average time/residue: 0.0591 time to fit residues: 2.9759 Evaluate side-chains 39 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain B residue 109 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 27 optimal weight: 0.2980 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 2 optimal weight: 0.1980 chunk 30 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 26 optimal weight: 0.1980 chunk 9 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.087385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.059101 restraints weight = 22469.081| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 5.04 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3258 Z= 0.134 Angle : 0.569 8.309 4424 Z= 0.280 Chirality : 0.039 0.168 492 Planarity : 0.004 0.031 562 Dihedral : 3.360 17.755 455 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.46 % Allowed : 10.20 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.88 (0.42), residues: 407 helix: 3.36 (0.36), residues: 189 sheet: 1.05 (0.76), residues: 42 loop : 0.55 (0.49), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 22 TYR 0.012 0.001 TYR A 23 PHE 0.011 0.001 PHE B 50 TRP 0.006 0.001 TRP A 270 HIS 0.002 0.000 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 3257) covalent geometry : angle 0.56959 / 0.28 ( 4422) SS BOND : bond 0.00066 / 0.03 ( 1) SS BOND : angle 0.20861 / 0.14 ( 2) hydrogen bonds : bond 0.02750 / 1.87 ( 202) hydrogen bonds : angle 4.00452 / 3.09 ( 577) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.124 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.9418 (mp) cc_final: 0.9058 (tp) REVERT: A 90 LYS cc_start: 0.8964 (tptt) cc_final: 0.8565 (tptt) REVERT: A 119 HIS cc_start: 0.8561 (t70) cc_final: 0.7717 (t70) REVERT: A 123 GLU cc_start: 0.8901 (pt0) cc_final: 0.8286 (pt0) REVERT: A 205 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8191 (tm-30) REVERT: A 296 TYR cc_start: 0.6082 (p90) cc_final: 0.5777 (p90) outliers start: 5 outliers final: 5 residues processed: 39 average time/residue: 0.0585 time to fit residues: 2.9522 Evaluate side-chains 39 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 109 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.1980 chunk 11 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 0.3980 chunk 5 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.0270 chunk 37 optimal weight: 0.7980 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.087556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.059838 restraints weight = 18475.768| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 4.60 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3258 Z= 0.124 Angle : 0.565 8.303 4424 Z= 0.279 Chirality : 0.038 0.175 492 Planarity : 0.004 0.031 562 Dihedral : 3.346 17.103 455 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.46 % Allowed : 10.79 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.89 (0.42), residues: 407 helix: 3.32 (0.36), residues: 189 sheet: 1.12 (0.76), residues: 42 loop : 0.60 (0.49), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 22 TYR 0.013 0.001 TYR A 23 PHE 0.009 0.001 PHE B 50 TRP 0.006 0.001 TRP A 270 HIS 0.001 0.000 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 3257) covalent geometry : angle 0.56553 / 0.28 ( 4422) SS BOND : bond 0.00079 / 0.04 ( 1) SS BOND : angle 0.22265 / 0.15 ( 2) hydrogen bonds : bond 0.02731 / 1.84 ( 202) hydrogen bonds : angle 3.98361 / 3.09 ( 577) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1319.08 seconds wall clock time: 23 minutes 17.38 seconds (1397.38 seconds total)