Starting phenix.real_space_refine on Thu Jul 2 00:05:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8de8_27387/07_2026/8de8_27387.cif Found real_map, /net/cci-nas-00/data/ceres_data/8de8_27387/07_2026/8de8_27387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8de8_27387/07_2026/8de8_27387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8de8_27387/07_2026/8de8_27387.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8de8_27387/07_2026/8de8_27387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8de8_27387/07_2026/8de8_27387.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8de8_27387/07_2026/8de8_27387.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8de8_27387/07_2026/8de8_27387.cif" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 4 8.98 5 P 4 5.49 5 S 16 5.16 5 C 3014 2.51 5 N 676 2.21 5 O 784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4498 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2168 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 7, 'TRANS': 268} Chain: "A" Number of atoms: 2168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2168 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 7, 'TRANS': 268} Chain: "B" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'D21': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 83 Unusual residues: {' K': 4, 'D21': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Time building chain proxies: 1.29, per 1000 atoms: 0.29 Number of scatterers: 4498 At special positions: 0 Unit cell: (90.738, 85.626, 94.572, 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) K 4 19.00 S 16 16.00 P 4 15.00 O 784 8.00 N 676 7.00 C 3014 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS A 93 " distance=2.01 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: 0.47 Conformation dependent library (CDL) restraints added in 175.8 milliseconds 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1004 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 80.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'B' and resid 43 through 91 Proline residue: B 71 - end of helix Processing helix chain 'B' and resid 95 through 112 Processing helix chain 'B' and resid 128 through 142 Processing helix chain 'B' and resid 152 through 197 Proline residue: B 168 - end of helix Processing helix chain 'B' and resid 205 through 223 Processing helix chain 'B' and resid 223 through 235 removed outlier: 3.735A pdb=" N LEU B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 250 Processing helix chain 'B' and resid 269 through 315 removed outlier: 3.656A pdb=" N ALA B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 91 Proline residue: A 71 - end of helix Processing helix chain 'A' and resid 95 through 112 Processing helix chain 'A' and resid 128 through 142 Processing helix chain 'A' and resid 152 through 197 Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 205 through 223 Processing helix chain 'A' and resid 223 through 235 removed outlier: 3.735A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 250 Processing helix chain 'A' and resid 269 through 315 removed outlier: 3.657A pdb=" N ALA A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA A 315 " --> pdb=" O ARG A 311 " (cutoff:3.500A) 360 hydrogen bonds defined for protein. 1080 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: 0.48 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 676 1.32 - 1.44: 1268 1.44 - 1.57: 2618 1.57 - 1.70: 12 1.70 - 1.83: 26 Bond restraints: 4600 Sorted by residual: bond pdb=" C31 D21 B 402 " pdb=" O30 D21 B 402 " ideal model delta sigma weight residual 1.327 1.429 -0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" C31 D21 A 402 " pdb=" O30 D21 A 402 " ideal model delta sigma weight residual 1.327 1.429 -0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" C31 D21 A 401 " pdb=" O30 D21 A 401 " ideal model delta sigma weight residual 1.327 1.426 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C31 D21 B 401 " pdb=" O30 D21 B 401 " ideal model delta sigma weight residual 1.327 1.426 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C16 D21 B 402 " pdb=" O18 D21 B 402 " ideal model delta sigma weight residual 1.326 1.405 -0.079 2.00e-02 2.50e+03 1.57e+01 ... (remaining 4595 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.26: 6170 6.26 - 12.53: 32 12.53 - 18.79: 0 18.79 - 25.06: 0 25.06 - 31.32: 8 Bond angle restraints: 6210 Sorted by residual: angle pdb=" C40 D21 A 402 " pdb=" C41 D21 A 402 " pdb=" C42 D21 A 402 " ideal model delta sigma weight residual 124.91 156.23 -31.32 3.00e+00 1.11e-01 1.09e+02 angle pdb=" C40 D21 B 402 " pdb=" C41 D21 B 402 " pdb=" C42 D21 B 402 " ideal model delta sigma weight residual 124.91 156.17 -31.26 3.00e+00 1.11e-01 1.09e+02 angle pdb=" C39 D21 B 402 " pdb=" C40 D21 B 402 " pdb=" C41 D21 B 402 " ideal model delta sigma weight residual 125.05 156.11 -31.06 3.00e+00 1.11e-01 1.07e+02 angle pdb=" C39 D21 A 402 " pdb=" C40 D21 A 402 " pdb=" C41 D21 A 402 " ideal model delta sigma weight residual 125.05 156.05 -31.00 3.00e+00 1.11e-01 1.07e+02 angle pdb=" C40 D21 A 401 " pdb=" C41 D21 A 401 " pdb=" C42 D21 A 401 " ideal model delta sigma weight residual 124.91 154.65 -29.74 3.00e+00 1.11e-01 9.83e+01 ... (remaining 6205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 2563 35.98 - 71.96: 112 71.96 - 107.94: 14 107.94 - 143.91: 4 143.91 - 179.89: 8 Dihedral angle restraints: 2701 sinusoidal: 1131 harmonic: 1570 Sorted by residual: dihedral pdb=" O22 D21 B 401 " pdb=" C20 D21 B 401 " pdb=" C21 D21 B 401 " pdb=" O30 D21 B 401 " ideal model delta sinusoidal sigma weight residual -61.77 118.12 -179.89 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O22 D21 A 401 " pdb=" C20 D21 A 401 " pdb=" C21 D21 A 401 " pdb=" O30 D21 A 401 " ideal model delta sinusoidal sigma weight residual -61.77 118.12 -179.89 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O22 D21 B 402 " pdb=" C20 D21 B 402 " pdb=" C21 D21 B 402 " pdb=" O30 D21 B 402 " ideal model delta sinusoidal sigma weight residual 298.23 123.53 174.70 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 2698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 607 0.076 - 0.151: 93 0.151 - 0.227: 4 0.227 - 0.302: 0 0.302 - 0.377: 6 Chirality restraints: 710 Sorted by residual: chirality pdb=" C20 D21 B 401 " pdb=" C19 D21 B 401 " pdb=" C21 D21 B 401 " pdb=" O30 D21 B 401 " both_signs ideal model delta sigma weight residual False 2.18 2.55 -0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" C20 D21 A 401 " pdb=" C19 D21 A 401 " pdb=" C21 D21 A 401 " pdb=" O30 D21 A 401 " both_signs ideal model delta sigma weight residual False 2.18 2.55 -0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" C20 D21 B 402 " pdb=" C19 D21 B 402 " pdb=" C21 D21 B 402 " pdb=" O30 D21 B 402 " both_signs ideal model delta sigma weight residual False 2.18 2.54 -0.36 2.00e-01 2.50e+01 3.29e+00 ... (remaining 707 not shown) Planarity restraints: 742 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 271 " 0.042 5.00e-02 4.00e+02 6.36e-02 6.48e+00 pdb=" N PRO B 272 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 272 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 272 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 271 " -0.042 5.00e-02 4.00e+02 6.35e-02 6.45e+00 pdb=" N PRO A 272 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 272 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 272 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 149 " 0.039 5.00e-02 4.00e+02 5.96e-02 5.69e+00 pdb=" N PRO B 150 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 150 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 150 " 0.033 5.00e-02 4.00e+02 ... (remaining 739 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.79: 958 2.79 - 3.38: 5309 3.38 - 3.96: 8284 3.96 - 4.55: 11341 4.55 - 5.14: 16843 Nonbonded interactions: 42735 Sorted by model distance: nonbonded pdb=" O ARG B 297 " pdb=" OG SER B 300 " model vdw 2.200 3.040 nonbonded pdb=" O GLY B 137 " pdb=" OG1 THR B 141 " model vdw 2.205 3.040 nonbonded pdb=" O GLY A 137 " pdb=" OG1 THR A 141 " model vdw 2.205 3.040 nonbonded pdb=" O ARG A 297 " pdb=" OG SER A 300 " model vdw 2.248 3.040 nonbonded pdb=" OE1 GLN A 76 " pdb=" NH2 ARG A 79 " model vdw 2.305 3.120 ... (remaining 42730 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 402) selection = chain 'B' } 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: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.620 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 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 : 0.008 0.102 4601 Z= 0.399 Angle : 1.553 31.321 6212 Z= 0.641 Chirality : 0.061 0.377 710 Planarity : 0.008 0.064 742 Dihedral : 22.624 179.892 1694 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.43 % Allowed : 0.86 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.33), residues: 548 helix: 2.16 (0.23), residues: 436 sheet: None (None), residues: 0 loop : -1.13 (0.52), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 79 TYR 0.018 0.003 TYR A 78 PHE 0.027 0.003 PHE A 285 TRP 0.038 0.003 TRP B 275 HIS 0.012 0.002 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00792 / 0.40 ( 4600) covalent geometry : angle 1.55229 / 0.64 ( 6210) SS BOND : bond 0.01915 / 1.01 ( 1) SS BOND : angle 3.23343 / 1.70 ( 2) hydrogen bonds : bond 0.10823 / 7.20 ( 360) hydrogen bonds : angle 4.76237 / 3.54 ( 1080) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 193 time to evaluate : 0.165 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 195 average time/residue: 0.4286 time to fit residues: 87.1849 Evaluate side-chains 133 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain A residue 267 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.2980 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 76 GLN B 95 GLN B 115 ASN B 122 GLN B 313 HIS A 76 GLN A 95 GLN A 115 ASN A 122 GLN A 313 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.139236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.091620 restraints weight = 6138.753| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.69 r_work: 0.2953 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4601 Z= 0.162 Angle : 0.753 11.009 6212 Z= 0.373 Chirality : 0.041 0.132 710 Planarity : 0.005 0.043 742 Dihedral : 24.338 171.889 740 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.45 % Allowed : 20.47 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.57 (0.35), residues: 548 helix: 3.20 (0.23), residues: 438 sheet: None (None), residues: 0 loop : -1.44 (0.54), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 79 TYR 0.015 0.002 TYR A 78 PHE 0.012 0.001 PHE B 158 TRP 0.031 0.002 TRP B 275 HIS 0.006 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 ( 4600) covalent geometry : angle 0.72889 / 0.36 ( 6210) SS BOND : bond 0.00597 / 0.31 ( 1) SS BOND : angle 10.51067 / 5.52 ( 2) hydrogen bonds : bond 0.05150 / 3.38 ( 360) hydrogen bonds : angle 3.84987 / 2.86 ( 1080) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.177 Fit side-chains REVERT: B 98 GLU cc_start: 0.8707 (mp0) cc_final: 0.8419 (pm20) REVERT: B 126 MET cc_start: 0.8874 (tmm) cc_final: 0.8620 (tmm) REVERT: A 98 GLU cc_start: 0.8708 (mp0) cc_final: 0.8420 (pm20) REVERT: A 126 MET cc_start: 0.8895 (tmm) cc_final: 0.8641 (tmm) outliers start: 16 outliers final: 6 residues processed: 151 average time/residue: 0.3981 time to fit residues: 62.7808 Evaluate side-chains 131 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 125 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 48 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 8 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 122 GLN A 122 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.136357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.087698 restraints weight = 6099.956| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.71 r_work: 0.2890 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4601 Z= 0.179 Angle : 0.707 8.459 6212 Z= 0.351 Chirality : 0.042 0.131 710 Planarity : 0.004 0.039 742 Dihedral : 22.456 167.697 736 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.36 % Allowed : 2.55 % Favored : 97.08 % Rotamer: Outliers : 4.09 % Allowed : 22.41 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.64 (0.36), residues: 548 helix: 3.29 (0.24), residues: 438 sheet: None (None), residues: 0 loop : -1.65 (0.54), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 79 TYR 0.012 0.002 TYR A 243 PHE 0.023 0.002 PHE A 214 TRP 0.035 0.002 TRP B 275 HIS 0.004 0.001 HIS B 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 ( 4600) covalent geometry : angle 0.69301 / 0.34 ( 6210) SS BOND : bond 0.01757 / 0.92 ( 1) SS BOND : angle 7.88366 / 4.14 ( 2) hydrogen bonds : bond 0.05109 / 3.33 ( 360) hydrogen bonds : angle 3.79005 / 2.81 ( 1080) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.170 Fit side-chains REVERT: B 90 MET cc_start: 0.9113 (tmm) cc_final: 0.8667 (tmm) REVERT: A 90 MET cc_start: 0.9121 (tmm) cc_final: 0.8813 (tmm) outliers start: 19 outliers final: 7 residues processed: 132 average time/residue: 0.3966 time to fit residues: 54.7842 Evaluate side-chains 122 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 282 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 8 optimal weight: 0.0770 chunk 37 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.136801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.088184 restraints weight = 6065.294| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.64 r_work: 0.2891 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4601 Z= 0.166 Angle : 0.697 8.463 6212 Z= 0.346 Chirality : 0.041 0.142 710 Planarity : 0.004 0.037 742 Dihedral : 19.742 159.967 736 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.36 % Allowed : 2.55 % Favored : 97.08 % Rotamer: Outliers : 3.02 % Allowed : 21.77 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.71 (0.37), residues: 548 helix: 3.35 (0.24), residues: 438 sheet: None (None), residues: 0 loop : -1.68 (0.55), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 79 TYR 0.011 0.001 TYR B 243 PHE 0.015 0.001 PHE B 214 TRP 0.028 0.001 TRP B 275 HIS 0.002 0.001 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 ( 4600) covalent geometry : angle 0.68861 / 0.34 ( 6210) SS BOND : bond 0.00608 / 0.32 ( 1) SS BOND : angle 5.96506 / 3.14 ( 2) hydrogen bonds : bond 0.04910 / 3.20 ( 360) hydrogen bonds : angle 3.75920 / 2.78 ( 1080) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: B 90 MET cc_start: 0.9074 (tmm) cc_final: 0.8626 (tmm) REVERT: A 90 MET cc_start: 0.9083 (tmm) cc_final: 0.8638 (tmm) REVERT: A 275 TRP cc_start: 0.8108 (m100) cc_final: 0.7845 (t-100) outliers start: 14 outliers final: 6 residues processed: 129 average time/residue: 0.3753 time to fit residues: 50.6892 Evaluate side-chains 120 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 114 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 282 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 36 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 122 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.134020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.085418 restraints weight = 6141.653| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.65 r_work: 0.2843 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 4601 Z= 0.205 Angle : 0.715 9.939 6212 Z= 0.350 Chirality : 0.042 0.136 710 Planarity : 0.004 0.037 742 Dihedral : 18.845 159.982 736 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.36 % Allowed : 2.55 % Favored : 97.08 % Rotamer: Outliers : 3.45 % Allowed : 22.84 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.71 (0.37), residues: 548 helix: 3.32 (0.24), residues: 438 sheet: None (None), residues: 0 loop : -1.51 (0.54), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 79 TYR 0.013 0.002 TYR B 243 PHE 0.014 0.001 PHE A 214 TRP 0.025 0.001 TRP B 275 HIS 0.003 0.001 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.20 ( 4600) covalent geometry : angle 0.71476 / 0.35 ( 6210) SS BOND : bond 0.00382 / 0.20 ( 1) SS BOND : angle 0.99290 / 0.52 ( 2) hydrogen bonds : bond 0.05183 / 3.37 ( 360) hydrogen bonds : angle 3.76467 / 2.79 ( 1080) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.191 Fit side-chains REVERT: B 56 LEU cc_start: 0.8662 (tp) cc_final: 0.8310 (tm) REVERT: B 60 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8181 (mp) REVERT: B 90 MET cc_start: 0.9013 (tmm) cc_final: 0.8630 (tmm) REVERT: B 115 ASN cc_start: 0.9121 (t0) cc_final: 0.8910 (t0) REVERT: B 126 MET cc_start: 0.8963 (tmm) cc_final: 0.8658 (tmm) REVERT: A 56 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8115 (tm) REVERT: A 60 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8140 (mp) REVERT: A 90 MET cc_start: 0.9018 (tmm) cc_final: 0.8636 (tmm) REVERT: A 126 MET cc_start: 0.8964 (tmm) cc_final: 0.8675 (tmm) outliers start: 16 outliers final: 10 residues processed: 136 average time/residue: 0.4237 time to fit residues: 60.2880 Evaluate side-chains 131 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 298 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 43 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 0.0060 chunk 1 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.137311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.088325 restraints weight = 6222.429| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.68 r_work: 0.2886 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4601 Z= 0.160 Angle : 0.717 10.268 6212 Z= 0.358 Chirality : 0.041 0.133 710 Planarity : 0.004 0.037 742 Dihedral : 17.866 157.225 736 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.36 % Allowed : 1.82 % Favored : 97.81 % Rotamer: Outliers : 4.31 % Allowed : 21.55 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.72 (0.37), residues: 548 helix: 3.29 (0.24), residues: 440 sheet: None (None), residues: 0 loop : -1.41 (0.55), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 79 TYR 0.011 0.002 TYR B 162 PHE 0.012 0.001 PHE A 214 TRP 0.029 0.001 TRP A 275 HIS 0.002 0.000 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 4600) covalent geometry : angle 0.71267 / 0.36 ( 6210) SS BOND : bond 0.00718 / 0.38 ( 1) SS BOND : angle 4.37298 / 2.30 ( 2) hydrogen bonds : bond 0.04697 / 3.04 ( 360) hydrogen bonds : angle 3.63759 / 2.70 ( 1080) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.166 Fit side-chains REVERT: B 90 MET cc_start: 0.9119 (tmm) cc_final: 0.8829 (tmm) REVERT: B 115 ASN cc_start: 0.9089 (t0) cc_final: 0.8876 (t0) REVERT: B 126 MET cc_start: 0.8920 (tmm) cc_final: 0.8582 (tmm) REVERT: A 56 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8268 (tm) REVERT: A 60 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8222 (mp) REVERT: A 90 MET cc_start: 0.9122 (tmm) cc_final: 0.8834 (tmm) REVERT: A 126 MET cc_start: 0.8898 (tmm) cc_final: 0.8568 (tmm) outliers start: 20 outliers final: 9 residues processed: 131 average time/residue: 0.3687 time to fit residues: 50.8339 Evaluate side-chains 126 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 275 TRP Chi-restraints excluded: chain A residue 282 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 122 GLN A 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.136697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.087497 restraints weight = 6188.428| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.66 r_work: 0.2874 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4601 Z= 0.172 Angle : 0.718 11.012 6212 Z= 0.357 Chirality : 0.041 0.133 710 Planarity : 0.004 0.038 742 Dihedral : 17.481 157.342 736 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.36 % Allowed : 2.92 % Favored : 96.72 % Rotamer: Outliers : 3.45 % Allowed : 24.78 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.64 (0.37), residues: 548 helix: 3.25 (0.24), residues: 440 sheet: None (None), residues: 0 loop : -1.49 (0.56), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 79 TYR 0.011 0.002 TYR A 243 PHE 0.011 0.001 PHE B 214 TRP 0.027 0.001 TRP A 275 HIS 0.002 0.001 HIS B 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 ( 4600) covalent geometry : angle 0.71557 / 0.36 ( 6210) SS BOND : bond 0.00332 / 0.17 ( 1) SS BOND : angle 3.51797 / 1.85 ( 2) hydrogen bonds : bond 0.04830 / 3.15 ( 360) hydrogen bonds : angle 3.70656 / 2.74 ( 1080) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.171 Fit side-chains REVERT: B 78 TYR cc_start: 0.8756 (m-80) cc_final: 0.8535 (m-80) REVERT: B 104 LYS cc_start: 0.8909 (mtmm) cc_final: 0.8511 (mtmm) REVERT: B 115 ASN cc_start: 0.9082 (t0) cc_final: 0.8845 (t0) REVERT: B 126 MET cc_start: 0.8870 (tmm) cc_final: 0.8561 (tmm) REVERT: A 56 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8270 (tm) REVERT: A 60 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8238 (mp) REVERT: A 104 LYS cc_start: 0.8925 (mtmm) cc_final: 0.8530 (mtmm) REVERT: A 126 MET cc_start: 0.8881 (tmm) cc_final: 0.8577 (tmm) outliers start: 16 outliers final: 9 residues processed: 130 average time/residue: 0.4172 time to fit residues: 56.7772 Evaluate side-chains 129 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 275 TRP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 275 TRP Chi-restraints excluded: chain A residue 282 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 26 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 0.0980 chunk 38 optimal weight: 0.7980 chunk 39 optimal weight: 0.1980 chunk 51 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 49 optimal weight: 0.0010 chunk 46 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 overall best weight: 0.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.139332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.090149 restraints weight = 6172.742| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.68 r_work: 0.2910 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4601 Z= 0.154 Angle : 0.752 11.578 6212 Z= 0.362 Chirality : 0.040 0.151 710 Planarity : 0.004 0.038 742 Dihedral : 16.991 156.309 736 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.36 % Allowed : 2.19 % Favored : 97.45 % Rotamer: Outliers : 3.23 % Allowed : 25.00 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.85 (0.37), residues: 548 helix: 3.32 (0.24), residues: 442 sheet: None (None), residues: 0 loop : -1.17 (0.58), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 79 TYR 0.011 0.001 TYR A 162 PHE 0.011 0.001 PHE B 158 TRP 0.026 0.001 TRP A 275 HIS 0.001 0.000 HIS B 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 4600) covalent geometry : angle 0.75062 / 0.36 ( 6210) SS BOND : bond 0.00319 / 0.17 ( 1) SS BOND : angle 2.38012 / 1.25 ( 2) hydrogen bonds : bond 0.04448 / 2.88 ( 360) hydrogen bonds : angle 3.64082 / 2.70 ( 1080) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.176 Fit side-chains REVERT: B 90 MET cc_start: 0.9001 (tpt) cc_final: 0.8799 (tmm) REVERT: B 126 MET cc_start: 0.8893 (tmm) cc_final: 0.8598 (tmm) REVERT: A 56 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8313 (tm) REVERT: A 78 TYR cc_start: 0.8720 (m-80) cc_final: 0.8493 (m-80) REVERT: A 90 MET cc_start: 0.8998 (tpt) cc_final: 0.8795 (tmm) REVERT: A 126 MET cc_start: 0.8904 (tmm) cc_final: 0.8606 (tmm) outliers start: 15 outliers final: 9 residues processed: 122 average time/residue: 0.4101 time to fit residues: 52.4503 Evaluate side-chains 134 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 275 TRP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 275 TRP Chi-restraints excluded: chain A residue 282 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 0.0030 chunk 50 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 122 GLN A 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.136979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.087763 restraints weight = 6177.496| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.67 r_work: 0.2875 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4601 Z= 0.172 Angle : 0.766 12.324 6212 Z= 0.368 Chirality : 0.041 0.134 710 Planarity : 0.004 0.040 742 Dihedral : 16.856 157.555 736 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.47 % Favored : 96.17 % Rotamer: Outliers : 3.02 % Allowed : 25.00 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.68 (0.37), residues: 548 helix: 3.25 (0.24), residues: 440 sheet: None (None), residues: 0 loop : -1.36 (0.56), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 79 TYR 0.010 0.002 TYR A 243 PHE 0.010 0.001 PHE A 158 TRP 0.025 0.001 TRP A 275 HIS 0.002 0.000 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.17 ( 4600) covalent geometry : angle 0.76480 / 0.37 ( 6210) SS BOND : bond 0.00276 / 0.15 ( 1) SS BOND : angle 2.47047 / 1.30 ( 2) hydrogen bonds : bond 0.04685 / 3.02 ( 360) hydrogen bonds : angle 3.71472 / 2.76 ( 1080) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.181 Fit side-chains REVERT: B 115 ASN cc_start: 0.9068 (t0) cc_final: 0.8820 (t0) REVERT: B 126 MET cc_start: 0.8903 (tmm) cc_final: 0.8600 (tmm) REVERT: A 126 MET cc_start: 0.8919 (tmm) cc_final: 0.8618 (tmm) outliers start: 14 outliers final: 8 residues processed: 135 average time/residue: 0.4662 time to fit residues: 65.4030 Evaluate side-chains 123 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 275 TRP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 275 TRP Chi-restraints excluded: chain A residue 282 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 21 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 16 optimal weight: 0.0470 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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 = 0.3781 r_free = 0.3781 target = 0.137764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.088366 restraints weight = 6161.993| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.72 r_work: 0.2882 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 4601 Z= 0.183 Angle : 0.870 13.714 6212 Z= 0.421 Chirality : 0.041 0.150 710 Planarity : 0.005 0.041 742 Dihedral : 16.678 157.557 736 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.36 % Allowed : 2.74 % Favored : 96.90 % Rotamer: Outliers : 2.59 % Allowed : 27.37 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.60 (0.37), residues: 548 helix: 3.19 (0.24), residues: 440 sheet: None (None), residues: 0 loop : -1.38 (0.55), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 79 TYR 0.011 0.002 TYR A 78 PHE 0.010 0.001 PHE A 158 TRP 0.026 0.001 TRP A 275 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.18 ( 4600) covalent geometry : angle 0.86883 / 0.42 ( 6210) SS BOND : bond 0.00265 / 0.14 ( 1) SS BOND : angle 2.28336 / 1.20 ( 2) hydrogen bonds : bond 0.04696 / 2.99 ( 360) hydrogen bonds : angle 3.75375 / 2.80 ( 1080) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 104 LYS cc_start: 0.8815 (mtmm) cc_final: 0.8340 (mtmt) REVERT: B 126 MET cc_start: 0.8911 (tmm) cc_final: 0.8607 (tmm) REVERT: A 104 LYS cc_start: 0.8817 (mtmm) cc_final: 0.8344 (mtmt) REVERT: A 126 MET cc_start: 0.8913 (tmm) cc_final: 0.8609 (tmm) outliers start: 12 outliers final: 11 residues processed: 126 average time/residue: 0.4386 time to fit residues: 57.7389 Evaluate side-chains 136 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 275 TRP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 275 TRP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 313 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 3 optimal weight: 0.0980 chunk 44 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 ASN A 122 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.137251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.088289 restraints weight = 6174.956| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.70 r_work: 0.2881 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 4601 Z= 0.182 Angle : 0.867 13.198 6212 Z= 0.417 Chirality : 0.041 0.144 710 Planarity : 0.004 0.041 742 Dihedral : 16.559 157.830 736 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.36 % Allowed : 2.92 % Favored : 96.72 % Rotamer: Outliers : 3.45 % Allowed : 25.86 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.68 (0.37), residues: 548 helix: 3.19 (0.24), residues: 440 sheet: None (None), residues: 0 loop : -1.08 (0.62), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 79 TYR 0.011 0.002 TYR B 243 PHE 0.011 0.001 PHE A 158 TRP 0.025 0.001 TRP A 275 HIS 0.017 0.003 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.18 ( 4600) covalent geometry : angle 0.86624 / 0.42 ( 6210) SS BOND : bond 0.00311 / 0.16 ( 1) SS BOND : angle 1.85029 / 0.97 ( 2) hydrogen bonds : bond 0.04685 / 3.03 ( 360) hydrogen bonds : angle 3.79193 / 2.80 ( 1080) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1979.97 seconds wall clock time: 34 minutes 28.36 seconds (2068.36 seconds total)