Starting phenix.real_space_refine on Wed Jun 3 17:04:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xzx_72377/06_2026/9xzx_72377.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xzx_72377/06_2026/9xzx_72377.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xzx_72377/06_2026/9xzx_72377.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xzx_72377/06_2026/9xzx_72377.map" model { file = "/net/cci-nas-00/data/ceres_data/9xzx_72377/06_2026/9xzx_72377.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xzx_72377/06_2026/9xzx_72377.cif" } resolution = 3.1 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= 0.017 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 S 18 5.16 5 C 2343 2.51 5 N 639 2.21 5 O 733 1.98 5 H 3622 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7356 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3774 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 230} Chain: "C" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 1707 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "D" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1874 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.45, per 1000 atoms: 0.20 Number of scatterers: 7356 At special positions: 0 Unit cell: (63.13, 65.27, 112.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 18 16.00 O 733 8.00 N 639 7.00 C 2343 6.00 H 3622 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 134 " distance=2.03 Simple disulfide: pdb=" SG CYS C 38 " - pdb=" SG CYS C 111 " distance=2.04 Simple disulfide: pdb=" SG CYS D 38 " - pdb=" SG CYS D 111 " 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: 0.63 Conformation dependent library (CDL) restraints added in 294.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 146 " pdb="ZN ZN A 301 " - pdb=" ND1 HIS A 142 " 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 860 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 10 sheets defined 14.1% alpha, 40.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 45 through 51 Processing helix chain 'A' and resid 94 through 103 removed outlier: 3.687A pdb=" N TYR A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP A 103 " --> pdb=" O LYS A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 180 through 196 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 240 through 242 No H-bonds generated for 'chain 'A' and resid 240 through 242' Processing helix chain 'C' and resid 77 through 80 Processing helix chain 'C' and resid 102 through 106 Processing helix chain 'D' and resid 77 through 80 Processing helix chain 'D' and resid 102 through 106 removed outlier: 3.501A pdb=" N THR D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 62 removed outlier: 5.337A pdb=" N SER A 58 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N GLY A 110 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N THR A 60 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL A 108 " --> pdb=" O THR A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 66 removed outlier: 8.084A pdb=" N THR A 133 " --> pdb=" O ASP A 86 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N VAL A 88 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N MET A 135 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N THR A 90 " --> pdb=" O MET A 135 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 164 through 173 removed outlier: 5.220A pdb=" N ASN A 165 " --> pdb=" O GLU A 161 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLU A 161 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A 167 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 9.801A pdb=" N ILE A 254 " --> pdb=" O ASN A 154 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU A 156 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N VAL A 256 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ARG A 158 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N LEU A 258 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N TYR A 160 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 177 through 179 Processing sheet with id=AA5, first strand: chain 'C' and resid 19 through 23 removed outlier: 3.975A pdb=" N GLN C 19 " --> pdb=" O SER C 41 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 27 through 28 removed outlier: 6.770A pdb=" N SER C 50 " --> pdb=" O ASP C 66 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASP C 66 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TRP C 52 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 27 through 28 Processing sheet with id=AA8, first strand: chain 'D' and resid 20 through 23 Processing sheet with id=AA9, first strand: chain 'D' and resid 27 through 29 removed outlier: 6.328A pdb=" N ARG D 53 " --> pdb=" O LEU D 62 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N LEU D 62 " --> pdb=" O ARG D 53 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 27 through 29 removed outlier: 3.934A pdb=" N SER D 129 " --> pdb=" O GLY D 113 " (cutoff:3.500A) 149 hydrogen bonds defined for protein. 372 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: 1.33 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3622 1.03 - 1.23: 44 1.23 - 1.43: 1599 1.43 - 1.62: 2138 1.62 - 1.82: 30 Bond restraints: 7433 Sorted by residual: bond pdb=" CA ASN A 76 " pdb=" C ASN A 76 " ideal model delta sigma weight residual 1.530 1.520 0.010 1.10e-02 8.26e+03 7.84e-01 bond pdb=" C PRO A 228 " pdb=" N GLY A 229 " ideal model delta sigma weight residual 1.321 1.330 -0.009 1.12e-02 7.97e+03 6.07e-01 bond pdb=" CA ARG D 115 " pdb=" CB ARG D 115 " ideal model delta sigma weight residual 1.524 1.536 -0.011 1.53e-02 4.27e+03 5.29e-01 bond pdb=" N GLY D 50 " pdb=" CA GLY D 50 " ideal model delta sigma weight residual 1.456 1.447 0.008 1.16e-02 7.43e+03 4.90e-01 bond pdb=" CA VAL D 72 " pdb=" CB VAL D 72 " ideal model delta sigma weight residual 1.540 1.531 0.009 1.36e-02 5.41e+03 4.88e-01 ... (remaining 7428 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.93: 13364 6.93 - 13.86: 0 13.86 - 20.79: 0 20.79 - 27.71: 0 27.71 - 34.64: 3 Bond angle restraints: 13367 Sorted by residual: angle pdb=" C SER D 120 " pdb=" CA SER D 120 " pdb=" HA SER D 120 " ideal model delta sigma weight residual 109.00 74.36 34.64 3.00e+00 1.11e-01 1.33e+02 angle pdb=" CB SER D 120 " pdb=" CA SER D 120 " pdb=" HA SER D 120 " ideal model delta sigma weight residual 109.00 74.54 34.46 3.00e+00 1.11e-01 1.32e+02 angle pdb=" N SER D 120 " pdb=" CA SER D 120 " pdb=" HA SER D 120 " ideal model delta sigma weight residual 110.00 76.24 33.76 3.00e+00 1.11e-01 1.27e+02 angle pdb=" N SER D 120 " pdb=" CA SER D 120 " pdb=" C SER D 120 " ideal model delta sigma weight residual 108.60 112.31 -3.71 1.46e+00 4.69e-01 6.47e+00 angle pdb=" N TRP D 118 " pdb=" CA TRP D 118 " pdb=" CB TRP D 118 " ideal model delta sigma weight residual 113.65 110.68 2.97 1.47e+00 4.63e-01 4.08e+00 ... (remaining 13362 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 3287 18.00 - 36.01: 155 36.01 - 54.01: 59 54.01 - 72.02: 16 72.02 - 90.02: 6 Dihedral angle restraints: 3523 sinusoidal: 1903 harmonic: 1620 Sorted by residual: dihedral pdb=" C SER D 120 " pdb=" N SER D 120 " pdb=" CA SER D 120 " pdb=" CB SER D 120 " ideal model delta harmonic sigma weight residual -122.60 -132.46 9.86 0 2.50e+00 1.60e-01 1.55e+01 dihedral pdb=" N SER D 120 " pdb=" C SER D 120 " pdb=" CA SER D 120 " pdb=" CB SER D 120 " ideal model delta harmonic sigma weight residual 122.80 131.73 -8.93 0 2.50e+00 1.60e-01 1.28e+01 dihedral pdb=" CA ASP A 248 " pdb=" CB ASP A 248 " pdb=" CG ASP A 248 " pdb=" OD1 ASP A 248 " ideal model delta sinusoidal sigma weight residual -30.00 -88.37 58.37 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 3520 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 496 0.074 - 0.148: 52 0.148 - 0.221: 0 0.221 - 0.295: 0 0.295 - 0.368: 1 Chirality restraints: 549 Sorted by residual: chirality pdb=" CA SER D 120 " pdb=" N SER D 120 " pdb=" C SER D 120 " pdb=" CB SER D 120 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CA ILE A 139 " pdb=" N ILE A 139 " pdb=" C ILE A 139 " pdb=" CB ILE A 139 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA ILE A 213 " pdb=" N ILE A 213 " pdb=" C ILE A 213 " pdb=" CB ILE A 213 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 546 not shown) Planarity restraints: 1120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 89 " 0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO D 90 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO D 90 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 90 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 31 " -0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO A 32 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 32 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 32 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 65 " 0.004 2.00e-02 2.50e+03 8.90e-03 7.92e-01 pdb=" C ALA C 65 " -0.015 2.00e-02 2.50e+03 pdb=" O ALA C 65 " 0.006 2.00e-02 2.50e+03 pdb=" N ASP C 66 " 0.005 2.00e-02 2.50e+03 ... (remaining 1117 not shown) Histogram of nonbonded interaction distances: 1.32 - 1.98: 90 1.98 - 2.63: 9582 2.63 - 3.29: 22170 3.29 - 3.94: 28533 3.94 - 4.60: 44311 Nonbonded interactions: 104686 Sorted by model distance: nonbonded pdb=" OD2 ASP A 107 " pdb=" NE2 HIS A 146 " model vdw 1.321 2.950 nonbonded pdb=" O TYR A 136 " pdb="HE22 GLN A 181 " model vdw 1.485 2.450 nonbonded pdb=" OD1 ASN A 162 " pdb=" H THR A 260 " model vdw 1.543 2.450 nonbonded pdb=" HG1 THR A 207 " pdb=" OG1 THR A 259 " model vdw 1.557 2.450 nonbonded pdb=" H ASP A 79 " pdb=" O TYR A 85 " model vdw 1.560 2.450 ... (remaining 104681 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.450 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: 0.030 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.690 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5837 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.279 3816 Z= 0.251 Angle : 0.564 4.117 5151 Z= 0.338 Chirality : 0.044 0.368 549 Planarity : 0.003 0.029 662 Dihedral : 10.243 90.020 1404 Min Nonbonded Distance : 1.321 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.39), residues: 468 helix: -1.32 (0.73), residues: 38 sheet: -0.20 (0.36), residues: 188 loop : 0.53 (0.42), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 54 TYR 0.008 0.001 TYR A 52 PHE 0.009 0.001 PHE A 220 TRP 0.010 0.001 TRP A 221 HIS 0.003 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.14 ( 3811) covalent geometry : angle 0.56337 / 0.34 ( 5145) SS BOND : bond 0.00312 / 0.22 ( 3) SS BOND : angle 0.74962 / 0.41 ( 6) hydrogen bonds : bond 0.14556 / 9.57 ( 138) hydrogen bonds : angle 7.96753 / 5.57 ( 372) metal coordination : bond 0.27745 / 19.17 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 THR cc_start: 0.8440 (m) cc_final: 0.8019 (m) REVERT: A 54 ASP cc_start: 0.8135 (t0) cc_final: 0.7470 (t0) REVERT: A 75 TYR cc_start: 0.5750 (m-80) cc_final: 0.5455 (m-80) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.2148 time to fit residues: 35.7031 Evaluate side-chains 101 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 20.0000 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 HIS C 61 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.162997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.134031 restraints weight = 16891.553| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 4.74 r_work: 0.3860 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6097 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3816 Z= 0.154 Angle : 0.553 4.243 5151 Z= 0.307 Chirality : 0.047 0.363 549 Planarity : 0.004 0.029 662 Dihedral : 4.412 18.367 521 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.47 % Allowed : 8.80 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.39), residues: 468 helix: -0.72 (0.76), residues: 40 sheet: -0.12 (0.39), residues: 174 loop : 0.32 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 82 TYR 0.020 0.001 TYR C 53 PHE 0.009 0.002 PHE D 52 TRP 0.014 0.002 TRP C 52 HIS 0.017 0.003 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 3811) covalent geometry : angle 0.55268 / 0.31 ( 5145) SS BOND : bond 0.00344 / 0.24 ( 3) SS BOND : angle 0.68257 / 0.47 ( 6) hydrogen bonds : bond 0.04106 / 2.71 ( 138) hydrogen bonds : angle 6.35985 / 4.39 ( 372) metal coordination : bond 0.00421 / 0.29 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.7105 (tpp) cc_final: 0.6846 (tpp) REVERT: A 54 ASP cc_start: 0.8822 (t0) cc_final: 0.8197 (t0) REVERT: A 60 THR cc_start: 0.6997 (p) cc_final: 0.6728 (m) REVERT: A 75 TYR cc_start: 0.5823 (m-80) cc_final: 0.5557 (m-80) REVERT: A 236 LYS cc_start: 0.8103 (mttt) cc_final: 0.7819 (mtmt) REVERT: C 52 TRP cc_start: 0.7353 (m100) cc_final: 0.7057 (m100) REVERT: C 88 ASP cc_start: 0.7218 (t0) cc_final: 0.6640 (p0) REVERT: C 101 LEU cc_start: 0.8810 (mt) cc_final: 0.8567 (mt) REVERT: D 53 ARG cc_start: 0.8085 (mtm180) cc_final: 0.7732 (mtm110) outliers start: 6 outliers final: 5 residues processed: 108 average time/residue: 0.1871 time to fit residues: 23.9309 Evaluate side-chains 101 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain D residue 129 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.160579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.128794 restraints weight = 17238.013| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 5.14 r_work: 0.3798 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6181 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3816 Z= 0.149 Angle : 0.558 7.175 5151 Z= 0.306 Chirality : 0.047 0.377 549 Planarity : 0.004 0.030 662 Dihedral : 4.367 19.105 521 Min Nonbonded Distance : 1.555 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.71 % Allowed : 9.29 % Favored : 89.00 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.39), residues: 468 helix: -0.50 (0.75), residues: 40 sheet: -0.18 (0.38), residues: 177 loop : 0.43 (0.41), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 82 TYR 0.013 0.001 TYR A 237 PHE 0.008 0.002 PHE D 52 TRP 0.013 0.002 TRP D 118 HIS 0.004 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 ( 3811) covalent geometry : angle 0.55832 / 0.31 ( 5145) SS BOND : bond 0.00310 / 0.21 ( 3) SS BOND : angle 0.59142 / 0.34 ( 6) hydrogen bonds : bond 0.03809 / 2.51 ( 138) hydrogen bonds : angle 6.05945 / 4.13 ( 372) metal coordination : bond 0.00563 / 0.38 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.7447 (tpp) cc_final: 0.6984 (tpp) REVERT: A 54 ASP cc_start: 0.8889 (t0) cc_final: 0.8279 (t0) REVERT: A 236 LYS cc_start: 0.8098 (mttt) cc_final: 0.7741 (mtmt) REVERT: C 52 TRP cc_start: 0.7412 (m100) cc_final: 0.6900 (m100) REVERT: C 101 LEU cc_start: 0.8735 (mt) cc_final: 0.8449 (mt) REVERT: D 53 ARG cc_start: 0.8097 (mtm180) cc_final: 0.7681 (mtm110) REVERT: D 61 GLU cc_start: 0.7405 (pm20) cc_final: 0.7159 (pm20) outliers start: 7 outliers final: 6 residues processed: 99 average time/residue: 0.1782 time to fit residues: 21.1898 Evaluate side-chains 99 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain D residue 129 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 5 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 13 optimal weight: 0.1980 chunk 43 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 GLN A 181 GLN C 97 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.160328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.129071 restraints weight = 17370.799| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 5.04 r_work: 0.3805 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6190 moved from start: 0.5215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3816 Z= 0.126 Angle : 0.518 5.851 5151 Z= 0.285 Chirality : 0.046 0.367 549 Planarity : 0.003 0.032 662 Dihedral : 4.194 19.212 521 Min Nonbonded Distance : 1.699 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.22 % Allowed : 10.27 % Favored : 88.51 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.39), residues: 468 helix: -0.94 (0.71), residues: 46 sheet: -0.10 (0.38), residues: 184 loop : 0.40 (0.42), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 82 TYR 0.015 0.001 TYR C 53 PHE 0.006 0.001 PHE D 52 TRP 0.014 0.002 TRP D 118 HIS 0.003 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 3811) covalent geometry : angle 0.51764 / 0.28 ( 5145) SS BOND : bond 0.00265 / 0.18 ( 3) SS BOND : angle 0.47744 / 0.24 ( 6) hydrogen bonds : bond 0.03620 / 2.44 ( 138) hydrogen bonds : angle 5.92513 / 4.04 ( 372) metal coordination : bond 0.00224 / 0.16 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.7442 (tpp) cc_final: 0.6852 (tpp) REVERT: A 54 ASP cc_start: 0.8893 (t0) cc_final: 0.8296 (t0) REVERT: A 75 TYR cc_start: 0.6098 (m-80) cc_final: 0.5838 (m-80) REVERT: A 236 LYS cc_start: 0.7935 (mttt) cc_final: 0.7630 (mtmt) REVERT: A 238 LEU cc_start: 0.7261 (mt) cc_final: 0.6876 (mt) REVERT: C 52 TRP cc_start: 0.7484 (m100) cc_final: 0.6833 (m100) REVERT: C 88 ASP cc_start: 0.7657 (t70) cc_final: 0.7080 (p0) REVERT: D 49 MET cc_start: 0.4785 (mmt) cc_final: 0.4549 (mmt) REVERT: D 53 ARG cc_start: 0.8263 (mtm180) cc_final: 0.8005 (mtm110) outliers start: 5 outliers final: 5 residues processed: 97 average time/residue: 0.1835 time to fit residues: 21.1487 Evaluate side-chains 98 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain D residue 129 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 4 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.157035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.127560 restraints weight = 17097.729| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 4.84 r_work: 0.3783 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6205 moved from start: 0.5707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3816 Z= 0.136 Angle : 0.526 5.653 5151 Z= 0.286 Chirality : 0.046 0.367 549 Planarity : 0.003 0.032 662 Dihedral : 4.161 18.186 521 Min Nonbonded Distance : 1.631 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.71 % Allowed : 11.49 % Favored : 86.80 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.39), residues: 468 helix: -1.42 (0.65), residues: 52 sheet: -0.05 (0.40), residues: 170 loop : 0.27 (0.42), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 82 TYR 0.010 0.001 TYR C 53 PHE 0.009 0.001 PHE A 200 TRP 0.014 0.001 TRP D 118 HIS 0.002 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 3811) covalent geometry : angle 0.52619 / 0.29 ( 5145) SS BOND : bond 0.00267 / 0.18 ( 3) SS BOND : angle 0.69216 / 0.34 ( 6) hydrogen bonds : bond 0.03554 / 2.37 ( 138) hydrogen bonds : angle 5.78013 / 3.94 ( 372) metal coordination : bond 0.00268 / 0.19 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.7641 (tpp) cc_final: 0.7075 (tpp) REVERT: A 48 MET cc_start: 0.6932 (mmm) cc_final: 0.6487 (mmm) REVERT: A 52 TYR cc_start: 0.7369 (m-80) cc_final: 0.7104 (m-80) REVERT: A 54 ASP cc_start: 0.8913 (t0) cc_final: 0.8361 (t0) REVERT: A 236 LYS cc_start: 0.7955 (mttt) cc_final: 0.7663 (mtmt) REVERT: D 53 ARG cc_start: 0.8378 (mtm180) cc_final: 0.8077 (mtm110) outliers start: 7 outliers final: 5 residues processed: 96 average time/residue: 0.1957 time to fit residues: 22.3229 Evaluate side-chains 95 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain D residue 129 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 22 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 29 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 97 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.157040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.127821 restraints weight = 17382.968| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 4.76 r_work: 0.3790 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6236 moved from start: 0.5983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3816 Z= 0.128 Angle : 0.517 5.029 5151 Z= 0.279 Chirality : 0.046 0.365 549 Planarity : 0.003 0.033 662 Dihedral : 4.100 16.301 521 Min Nonbonded Distance : 1.673 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.22 % Allowed : 11.74 % Favored : 87.04 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.39), residues: 468 helix: -1.50 (0.64), residues: 52 sheet: -0.05 (0.40), residues: 170 loop : 0.27 (0.42), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 82 TYR 0.015 0.001 TYR A 198 PHE 0.006 0.001 PHE D 52 TRP 0.012 0.001 TRP D 118 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 3811) covalent geometry : angle 0.51737 / 0.28 ( 5145) SS BOND : bond 0.00272 / 0.18 ( 3) SS BOND : angle 0.55248 / 0.27 ( 6) hydrogen bonds : bond 0.03393 / 2.26 ( 138) hydrogen bonds : angle 5.74288 / 3.91 ( 372) metal coordination : bond 0.00136 / 0.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.7779 (tpp) cc_final: 0.7093 (tpp) REVERT: A 48 MET cc_start: 0.6998 (mmm) cc_final: 0.6626 (mmm) REVERT: A 54 ASP cc_start: 0.8849 (t0) cc_final: 0.8268 (t0) REVERT: A 200 PHE cc_start: 0.5756 (t80) cc_final: 0.5501 (t80) REVERT: A 236 LYS cc_start: 0.7986 (mttt) cc_final: 0.7722 (mtmt) REVERT: C 52 TRP cc_start: 0.7485 (m100) cc_final: 0.6619 (m100) REVERT: C 88 ASP cc_start: 0.7707 (t70) cc_final: 0.7138 (p0) REVERT: D 53 ARG cc_start: 0.8415 (mtm180) cc_final: 0.7991 (mtm110) outliers start: 5 outliers final: 4 residues processed: 100 average time/residue: 0.1885 time to fit residues: 22.1572 Evaluate side-chains 98 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain D residue 129 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.155949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.126915 restraints weight = 17619.020| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 4.76 r_work: 0.3769 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6241 moved from start: 0.6264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3816 Z= 0.141 Angle : 0.524 5.199 5151 Z= 0.283 Chirality : 0.046 0.365 549 Planarity : 0.003 0.033 662 Dihedral : 4.133 16.022 521 Min Nonbonded Distance : 1.691 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.73 % Allowed : 13.45 % Favored : 85.82 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.39), residues: 468 helix: -1.47 (0.64), residues: 52 sheet: 0.04 (0.40), residues: 171 loop : 0.14 (0.41), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 82 TYR 0.008 0.001 TYR A 198 PHE 0.008 0.001 PHE D 52 TRP 0.012 0.001 TRP D 118 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 3811) covalent geometry : angle 0.52423 / 0.28 ( 5145) SS BOND : bond 0.00263 / 0.17 ( 3) SS BOND : angle 0.62464 / 0.30 ( 6) hydrogen bonds : bond 0.03443 / 2.28 ( 138) hydrogen bonds : angle 5.75374 / 3.91 ( 372) metal coordination : bond 0.00022 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 94 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.7720 (tpp) cc_final: 0.6957 (tpp) REVERT: A 48 MET cc_start: 0.7092 (mmm) cc_final: 0.6606 (mmm) REVERT: A 54 ASP cc_start: 0.8890 (t0) cc_final: 0.8308 (t0) REVERT: A 236 LYS cc_start: 0.7964 (mttt) cc_final: 0.7714 (mtmt) REVERT: C 52 TRP cc_start: 0.7503 (m100) cc_final: 0.6663 (m100) REVERT: C 88 ASP cc_start: 0.7750 (t70) cc_final: 0.7181 (p0) REVERT: D 53 ARG cc_start: 0.8383 (mtm180) cc_final: 0.7922 (mtm110) outliers start: 3 outliers final: 3 residues processed: 96 average time/residue: 0.2011 time to fit residues: 22.7073 Evaluate side-chains 92 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 89 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain D residue 129 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 41 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.156090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.127383 restraints weight = 17883.144| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 4.78 r_work: 0.3767 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6226 moved from start: 0.6551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3816 Z= 0.129 Angle : 0.527 6.460 5151 Z= 0.284 Chirality : 0.046 0.364 549 Planarity : 0.003 0.034 662 Dihedral : 4.114 16.330 521 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.73 % Allowed : 14.43 % Favored : 84.84 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.39), residues: 468 helix: -1.52 (0.64), residues: 52 sheet: 0.07 (0.40), residues: 171 loop : 0.15 (0.41), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 54 TYR 0.008 0.001 TYR D 110 PHE 0.007 0.001 PHE D 52 TRP 0.011 0.002 TRP D 130 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 3811) covalent geometry : angle 0.52725 / 0.28 ( 5145) SS BOND : bond 0.00245 / 0.16 ( 3) SS BOND : angle 0.58238 / 0.27 ( 6) hydrogen bonds : bond 0.03350 / 2.22 ( 138) hydrogen bonds : angle 5.72233 / 3.88 ( 372) metal coordination : bond 0.00009 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.7677 (tpp) cc_final: 0.7013 (tpp) REVERT: A 54 ASP cc_start: 0.8878 (t0) cc_final: 0.8322 (t0) REVERT: A 200 PHE cc_start: 0.5602 (t80) cc_final: 0.5382 (t80) REVERT: A 221 TRP cc_start: 0.6912 (p-90) cc_final: 0.5526 (p-90) REVERT: A 236 LYS cc_start: 0.7964 (mttt) cc_final: 0.7669 (mtmt) REVERT: C 52 TRP cc_start: 0.7493 (m100) cc_final: 0.6653 (m100) REVERT: C 88 ASP cc_start: 0.7742 (t70) cc_final: 0.7018 (p0) REVERT: D 53 ARG cc_start: 0.8397 (mtm180) cc_final: 0.7459 (mtm110) REVERT: D 61 GLU cc_start: 0.7192 (pm20) cc_final: 0.6739 (pm20) outliers start: 3 outliers final: 3 residues processed: 92 average time/residue: 0.1750 time to fit residues: 19.2825 Evaluate side-chains 91 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 88 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain D residue 129 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 6 optimal weight: 0.4980 chunk 3 optimal weight: 0.7980 chunk 24 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.156477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.127910 restraints weight = 16957.500| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 4.65 r_work: 0.3779 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6214 moved from start: 0.6755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3816 Z= 0.122 Angle : 0.525 5.006 5151 Z= 0.280 Chirality : 0.046 0.364 549 Planarity : 0.003 0.034 662 Dihedral : 4.081 15.585 521 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.73 % Allowed : 15.40 % Favored : 83.86 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.39), residues: 468 helix: -1.49 (0.65), residues: 52 sheet: 0.06 (0.41), residues: 164 loop : 0.23 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 54 TYR 0.006 0.001 TYR D 110 PHE 0.007 0.001 PHE A 220 TRP 0.022 0.002 TRP D 130 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 3811) covalent geometry : angle 0.52483 / 0.28 ( 5145) SS BOND : bond 0.00246 / 0.15 ( 3) SS BOND : angle 0.58007 / 0.26 ( 6) hydrogen bonds : bond 0.03215 / 2.13 ( 138) hydrogen bonds : angle 5.67510 / 3.86 ( 372) metal coordination : bond 0.00016 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.7666 (tpp) cc_final: 0.6992 (tpp) REVERT: A 48 MET cc_start: 0.7148 (mmm) cc_final: 0.6775 (mmm) REVERT: A 54 ASP cc_start: 0.8889 (t0) cc_final: 0.8312 (t0) REVERT: A 221 TRP cc_start: 0.6896 (p-90) cc_final: 0.5559 (p-90) REVERT: A 236 LYS cc_start: 0.7976 (mttt) cc_final: 0.7666 (mtmt) REVERT: C 52 TRP cc_start: 0.7493 (m100) cc_final: 0.6731 (m100) REVERT: C 88 ASP cc_start: 0.7185 (t70) cc_final: 0.6754 (p0) REVERT: D 53 ARG cc_start: 0.8393 (mtm180) cc_final: 0.7906 (mtm110) outliers start: 3 outliers final: 3 residues processed: 92 average time/residue: 0.1975 time to fit residues: 21.5635 Evaluate side-chains 89 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain D residue 129 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 1 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 55 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.154322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.124110 restraints weight = 17473.150| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 4.91 r_work: 0.3729 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6236 moved from start: 0.6975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3816 Z= 0.155 Angle : 0.553 4.691 5151 Z= 0.297 Chirality : 0.047 0.364 549 Planarity : 0.004 0.033 662 Dihedral : 4.199 14.744 521 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.98 % Allowed : 16.14 % Favored : 82.89 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.39), residues: 468 helix: -1.55 (0.64), residues: 52 sheet: -0.15 (0.39), residues: 174 loop : 0.20 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 54 TYR 0.011 0.001 TYR C 53 PHE 0.014 0.002 PHE A 200 TRP 0.023 0.002 TRP D 130 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 ( 3811) covalent geometry : angle 0.55229 / 0.30 ( 5145) SS BOND : bond 0.00308 / 0.19 ( 3) SS BOND : angle 0.73935 / 0.36 ( 6) hydrogen bonds : bond 0.03432 / 2.27 ( 138) hydrogen bonds : angle 5.76539 / 3.94 ( 372) metal coordination : bond 0.00182 / 0.13 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.7661 (tpp) cc_final: 0.6965 (tpp) REVERT: A 52 TYR cc_start: 0.7536 (m-80) cc_final: 0.7313 (m-80) REVERT: A 54 ASP cc_start: 0.8950 (t0) cc_final: 0.8374 (t0) REVERT: A 221 TRP cc_start: 0.6942 (p-90) cc_final: 0.5604 (p-90) REVERT: A 236 LYS cc_start: 0.7982 (mttt) cc_final: 0.7684 (mtmt) REVERT: C 88 ASP cc_start: 0.6801 (OUTLIER) cc_final: 0.6362 (p0) REVERT: D 53 ARG cc_start: 0.8382 (mtm180) cc_final: 0.7456 (mtm110) REVERT: D 61 GLU cc_start: 0.7269 (pm20) cc_final: 0.6829 (pm20) outliers start: 4 outliers final: 3 residues processed: 92 average time/residue: 0.1960 time to fit residues: 21.3662 Evaluate side-chains 90 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain D residue 129 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 19 optimal weight: 0.4980 chunk 34 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.154979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.126506 restraints weight = 17161.787| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 4.61 r_work: 0.3757 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6271 moved from start: 0.7181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3816 Z= 0.136 Angle : 0.545 5.000 5151 Z= 0.292 Chirality : 0.046 0.365 549 Planarity : 0.003 0.034 662 Dihedral : 4.140 14.850 521 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.98 % Allowed : 16.38 % Favored : 82.64 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.38), residues: 468 helix: -1.50 (0.64), residues: 52 sheet: -0.10 (0.40), residues: 167 loop : 0.02 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 60 TYR 0.020 0.001 TYR C 121 PHE 0.012 0.001 PHE A 200 TRP 0.036 0.002 TRP D 130 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 3811) covalent geometry : angle 0.54471 / 0.29 ( 5145) SS BOND : bond 0.00303 / 0.18 ( 3) SS BOND : angle 0.68663 / 0.32 ( 6) hydrogen bonds : bond 0.03284 / 2.17 ( 138) hydrogen bonds : angle 5.74790 / 3.93 ( 372) metal coordination : bond 0.00115 / 0.08 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2587.03 seconds wall clock time: 44 minutes 36.14 seconds (2676.14 seconds total)