Starting phenix.real_space_refine on Tue Aug 4 11:46:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ggy_40025/08_2026/8ggy_40025.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ggy_40025/08_2026/8ggy_40025.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ggy_40025/08_2026/8ggy_40025.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ggy_40025/08_2026/8ggy_40025.map" model { file = "/net/cci-nas-00/data/ceres_data/8ggy_40025/08_2026/8ggy_40025.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ggy_40025/08_2026/8ggy_40025.cif" } resolution = 3.9 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= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 13 5.16 5 C 1388 2.51 5 N 339 2.21 5 O 356 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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2096 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2081 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 3, 'ASP:plan': 4, 'GLU:plan': 6, 'HIS:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 73 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.01, per 1000 atoms: 0.48 Number of scatterers: 2096 At special positions: 0 Unit cell: (54.6651, 85.9023, 62.4744, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 13 16.00 O 356 8.00 N 339 7.00 C 1388 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.34 Conformation dependent library (CDL) restraints added in 133.1 milliseconds 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 538 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 85.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'R' and resid 32 through 61 removed outlier: 3.619A pdb=" N MET R 36 " --> pdb=" O TRP R 32 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 86 Processing helix chain 'R' and resid 86 through 96 Processing helix chain 'R' and resid 103 through 137 removed outlier: 4.335A pdb=" N GLU R 107 " --> pdb=" O ASN R 103 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG R 131 " --> pdb=" O ILE R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 164 removed outlier: 3.690A pdb=" N ALA R 150 " --> pdb=" O THR R 146 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 171 removed outlier: 3.760A pdb=" N MET R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 187 Processing helix chain 'R' and resid 196 through 208 removed outlier: 3.719A pdb=" N ALA R 200 " --> pdb=" O ASN R 196 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE R 201 " --> pdb=" O GLN R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 237 Processing helix chain 'R' and resid 270 through 299 removed outlier: 3.788A pdb=" N THR R 274 " --> pdb=" O LYS R 270 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.774A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 316 Processing helix chain 'R' and resid 317 through 327 removed outlier: 3.584A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 340 removed outlier: 3.513A pdb=" N LEU R 340 " --> pdb=" O PHE R 336 " (cutoff:3.500A) 160 hydrogen bonds defined for protein. 480 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: 0.33 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 643 1.34 - 1.46: 589 1.46 - 1.58: 900 1.58 - 1.70: 0 1.70 - 1.82: 19 Bond restraints: 2151 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.453 -0.056 2.00e-02 2.50e+03 7.78e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.578 -0.055 2.00e-02 2.50e+03 7.56e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.443 -0.049 2.00e-02 2.50e+03 6.08e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.567 -0.047 2.00e-02 2.50e+03 5.51e+00 bond pdb=" CAI G1I R 501 " pdb=" NAN G1I R 501 " ideal model delta sigma weight residual 1.451 1.497 -0.046 2.00e-02 2.50e+03 5.21e+00 ... (remaining 2146 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 2843 1.38 - 2.75: 77 2.75 - 4.13: 19 4.13 - 5.51: 10 5.51 - 6.88: 2 Bond angle restraints: 2951 Sorted by residual: angle pdb=" C GLU R 180 " pdb=" N ALA R 181 " pdb=" CA ALA R 181 " ideal model delta sigma weight residual 121.54 128.17 -6.63 1.91e+00 2.74e-01 1.21e+01 angle pdb=" C VAL R 295 " pdb=" N HIS R 296 " pdb=" CA HIS R 296 " ideal model delta sigma weight residual 120.72 116.07 4.65 1.67e+00 3.59e-01 7.75e+00 angle pdb=" CB MET R 279 " pdb=" CG MET R 279 " pdb=" SD MET R 279 " ideal model delta sigma weight residual 112.70 119.58 -6.88 3.00e+00 1.11e-01 5.26e+00 angle pdb=" CA GLN R 337 " pdb=" CB GLN R 337 " pdb=" CG GLN R 337 " ideal model delta sigma weight residual 114.10 118.62 -4.52 2.00e+00 2.50e-01 5.10e+00 angle pdb=" C ASP R 300 " pdb=" N ASN R 301 " pdb=" CA ASN R 301 " ideal model delta sigma weight residual 123.05 126.33 -3.28 1.57e+00 4.06e-01 4.36e+00 ... (remaining 2946 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.70: 1088 15.70 - 31.39: 95 31.39 - 47.09: 32 47.09 - 62.78: 5 62.78 - 78.48: 4 Dihedral angle restraints: 1224 sinusoidal: 396 harmonic: 828 Sorted by residual: dihedral pdb=" CA PHE R 208 " pdb=" C PHE R 208 " pdb=" N TYR R 209 " pdb=" CA TYR R 209 " ideal model delta harmonic sigma weight residual 180.00 -164.67 -15.33 0 5.00e+00 4.00e-02 9.40e+00 dihedral pdb=" CA ARG R 131 " pdb=" CB ARG R 131 " pdb=" CG ARG R 131 " pdb=" CD ARG R 131 " ideal model delta sinusoidal sigma weight residual -180.00 -126.96 -53.04 3 1.50e+01 4.44e-03 9.17e+00 dihedral pdb=" CA ILE R 325 " pdb=" C ILE R 325 " pdb=" N TYR R 326 " pdb=" CA TYR R 326 " ideal model delta harmonic sigma weight residual 180.00 -165.11 -14.89 0 5.00e+00 4.00e-02 8.87e+00 ... (remaining 1221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 237 0.035 - 0.069: 91 0.069 - 0.103: 22 0.103 - 0.138: 3 0.138 - 0.172: 1 Chirality restraints: 354 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.57 -0.17 2.00e-01 2.50e+01 7.43e-01 chirality pdb=" CA ILE R 303 " pdb=" N ILE R 303 " pdb=" C ILE R 303 " pdb=" CB ILE R 303 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CB VAL R 295 " pdb=" CA VAL R 295 " pdb=" CG1 VAL R 295 " pdb=" CG2 VAL R 295 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.18e-01 ... (remaining 351 not shown) Planarity restraints: 363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER R 329 " -0.029 5.00e-02 4.00e+02 4.39e-02 3.08e+00 pdb=" N PRO R 330 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO R 330 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 330 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 198 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.31e+00 pdb=" C ALA R 198 " 0.020 2.00e-02 2.50e+03 pdb=" O ALA R 198 " -0.007 2.00e-02 2.50e+03 pdb=" N TYR R 199 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR R 281 " -0.004 2.00e-02 2.50e+03 8.53e-03 7.27e-01 pdb=" C THR R 281 " 0.015 2.00e-02 2.50e+03 pdb=" O THR R 281 " -0.006 2.00e-02 2.50e+03 pdb=" N PHE R 282 " -0.005 2.00e-02 2.50e+03 ... (remaining 360 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 784 2.88 - 3.39: 2232 3.39 - 3.89: 3300 3.89 - 4.40: 3172 4.40 - 4.90: 5820 Nonbonded interactions: 15308 Sorted by model distance: nonbonded pdb=" O ALA R 92 " pdb=" OG1 THR R 96 " model vdw 2.377 3.040 nonbonded pdb=" O TRP R 99 " pdb=" OG1 THR R 100 " model vdw 2.438 3.040 nonbonded pdb=" OD1 ASP R 130 " pdb=" N ARG R 131 " model vdw 2.481 3.120 nonbonded pdb=" O GLN R 337 " pdb=" OE1 GLN R 337 " model vdw 2.559 3.040 nonbonded pdb=" O ILE R 127 " pdb=" OD1 ASP R 130 " model vdw 2.585 3.040 ... (remaining 15303 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.020 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 2151 Z= 0.195 Angle : 0.631 6.883 2951 Z= 0.330 Chirality : 0.040 0.172 354 Planarity : 0.004 0.044 363 Dihedral : 14.743 78.477 686 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 2.19 (0.51), residues: 277 helix: 2.21 (0.36), residues: 217 sheet: None (None), residues: 0 loop : -1.51 (0.67), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 228 TYR 0.006 0.001 TYR R 326 PHE 0.009 0.001 PHE R 290 TRP 0.013 0.001 TRP R 109 HIS 0.002 0.001 HIS R 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.19 ( 2151) covalent geometry : angle 0.63075 / 0.33 ( 2951) hydrogen bonds : bond 0.13394 / 9.48 ( 160) hydrogen bonds : angle 4.58551 / 3.45 ( 480) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.079 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0546 time to fit residues: 2.9763 Evaluate side-chains 32 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3449 r_free = 0.3449 target = 0.127399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.114236 restraints weight = 3804.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.116988 restraints weight = 2043.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.118952 restraints weight = 1259.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.120311 restraints weight = 864.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.121205 restraints weight = 643.144| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2151 Z= 0.147 Angle : 0.570 5.733 2951 Z= 0.305 Chirality : 0.040 0.132 354 Planarity : 0.004 0.042 363 Dihedral : 3.981 15.414 312 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.63 % Allowed : 11.92 % Favored : 84.46 % 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: 2.11 (0.51), residues: 277 helix: 2.02 (0.35), residues: 223 sheet: None (None), residues: 0 loop : -1.31 (0.69), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG R 228 TYR 0.017 0.001 TYR R 308 PHE 0.016 0.001 PHE R 104 TRP 0.008 0.001 TRP R 109 HIS 0.001 0.000 HIS R 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 ( 2151) covalent geometry : angle 0.56979 / 0.31 ( 2951) hydrogen bonds : bond 0.05657 / 4.06 ( 160) hydrogen bonds : angle 3.72343 / 2.93 ( 480) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.073 Fit side-chains REVERT: R 339 LEU cc_start: 0.8491 (mm) cc_final: 0.8257 (mm) outliers start: 7 outliers final: 5 residues processed: 41 average time/residue: 0.0532 time to fit residues: 2.6647 Evaluate side-chains 37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 0.0020 chunk 17 optimal weight: 0.7980 chunk 26 optimal weight: 0.0870 overall best weight: 0.3366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 318 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.134345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.121218 restraints weight = 3741.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.123954 restraints weight = 1996.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.125996 restraints weight = 1236.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.127387 restraints weight = 845.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.128394 restraints weight = 627.616| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 2151 Z= 0.120 Angle : 0.535 5.297 2951 Z= 0.285 Chirality : 0.039 0.130 354 Planarity : 0.004 0.040 363 Dihedral : 3.867 15.346 312 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.66 % Allowed : 16.06 % Favored : 79.27 % 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: 2.20 (0.51), residues: 277 helix: 2.03 (0.35), residues: 226 sheet: None (None), residues: 0 loop : -1.21 (0.72), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 228 TYR 0.011 0.001 TYR R 308 PHE 0.018 0.001 PHE R 104 TRP 0.008 0.001 TRP R 109 HIS 0.001 0.000 HIS R 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.12 ( 2151) covalent geometry : angle 0.53492 / 0.29 ( 2951) hydrogen bonds : bond 0.05022 / 3.58 ( 160) hydrogen bonds : angle 3.57626 / 2.83 ( 480) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.084 Fit side-chains REVERT: R 318 ASN cc_start: 0.8534 (t0) cc_final: 0.8310 (t0) outliers start: 9 outliers final: 7 residues processed: 38 average time/residue: 0.0524 time to fit residues: 2.4389 Evaluate side-chains 37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 324 LEU Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 2 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 24 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 13 optimal weight: 0.0000 chunk 27 optimal weight: 0.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 318 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.127707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.114746 restraints weight = 3737.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.117357 restraints weight = 2038.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.119281 restraints weight = 1282.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.120616 restraints weight = 888.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.121613 restraints weight = 669.517| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2151 Z= 0.138 Angle : 0.555 5.985 2951 Z= 0.297 Chirality : 0.040 0.128 354 Planarity : 0.004 0.040 363 Dihedral : 3.924 15.331 312 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.15 % Allowed : 16.58 % Favored : 79.27 % 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: 2.19 (0.51), residues: 277 helix: 2.05 (0.35), residues: 225 sheet: None (None), residues: 0 loop : -1.31 (0.70), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 228 TYR 0.013 0.001 TYR R 308 PHE 0.018 0.001 PHE R 104 TRP 0.007 0.001 TRP R 109 HIS 0.001 0.001 HIS R 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 ( 2151) covalent geometry : angle 0.55499 / 0.30 ( 2951) hydrogen bonds : bond 0.05373 / 3.87 ( 160) hydrogen bonds : angle 3.60963 / 2.85 ( 480) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.079 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 33 average time/residue: 0.0588 time to fit residues: 2.3392 Evaluate side-chains 33 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 0.2980 chunk 13 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 0.4980 chunk 27 optimal weight: 0.3980 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.128536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.115618 restraints weight = 3751.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.118263 restraints weight = 2042.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.120183 restraints weight = 1280.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.121594 restraints weight = 885.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.122513 restraints weight = 656.323| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2151 Z= 0.126 Angle : 0.546 5.427 2951 Z= 0.291 Chirality : 0.039 0.132 354 Planarity : 0.004 0.039 363 Dihedral : 3.858 15.403 312 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.15 % Allowed : 18.13 % Favored : 77.72 % 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 (0.51), residues: 277 helix: 2.14 (0.35), residues: 225 sheet: None (None), residues: 0 loop : -1.39 (0.72), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 228 TYR 0.012 0.001 TYR R 308 PHE 0.017 0.001 PHE R 104 TRP 0.008 0.001 TRP R 109 HIS 0.001 0.000 HIS R 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.13 ( 2151) covalent geometry : angle 0.54587 / 0.29 ( 2951) hydrogen bonds : bond 0.05102 / 3.67 ( 160) hydrogen bonds : angle 3.57352 / 2.83 ( 480) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.080 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 33 average time/residue: 0.0616 time to fit residues: 2.4378 Evaluate side-chains 34 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 13 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 10 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 318 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.127381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.114429 restraints weight = 3715.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.117040 restraints weight = 2041.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.118955 restraints weight = 1281.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.120146 restraints weight = 884.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.121048 restraints weight = 669.345| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2151 Z= 0.147 Angle : 0.570 5.738 2951 Z= 0.306 Chirality : 0.040 0.131 354 Planarity : 0.004 0.040 363 Dihedral : 3.987 15.608 312 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 6.74 % Allowed : 18.65 % Favored : 74.61 % 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: 2.15 (0.50), residues: 277 helix: 2.06 (0.35), residues: 224 sheet: None (None), residues: 0 loop : -1.43 (0.72), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 228 TYR 0.014 0.001 TYR R 308 PHE 0.014 0.001 PHE R 104 TRP 0.006 0.001 TRP R 109 HIS 0.001 0.001 HIS R 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 ( 2151) covalent geometry : angle 0.57042 / 0.31 ( 2951) hydrogen bonds : bond 0.05754 / 4.17 ( 160) hydrogen bonds : angle 3.70577 / 2.92 ( 480) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 29 time to evaluate : 0.077 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 39 average time/residue: 0.0535 time to fit residues: 2.5373 Evaluate side-chains 35 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 279 MET Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 318 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.125419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.112516 restraints weight = 3870.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.115248 restraints weight = 2103.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.117192 restraints weight = 1308.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.118420 restraints weight = 896.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.119382 restraints weight = 667.543| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2151 Z= 0.143 Angle : 0.571 6.106 2951 Z= 0.305 Chirality : 0.040 0.131 354 Planarity : 0.004 0.040 363 Dihedral : 3.989 15.474 312 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 5.70 % Allowed : 18.65 % Favored : 75.65 % 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: 2.19 (0.50), residues: 277 helix: 2.05 (0.35), residues: 225 sheet: None (None), residues: 0 loop : -1.28 (0.71), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 228 TYR 0.013 0.001 TYR R 308 PHE 0.014 0.001 PHE R 104 TRP 0.007 0.001 TRP R 109 HIS 0.001 0.000 HIS R 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 2151) covalent geometry : angle 0.57144 / 0.30 ( 2951) hydrogen bonds : bond 0.05649 / 4.07 ( 160) hydrogen bonds : angle 3.69971 / 2.91 ( 480) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 28 time to evaluate : 0.075 Fit side-chains REVERT: R 339 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8197 (mm) outliers start: 11 outliers final: 8 residues processed: 35 average time/residue: 0.0584 time to fit residues: 2.4587 Evaluate side-chains 37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 279 MET Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 1 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 54.2995 > 50:) chunk 14 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 7 optimal weight: 0.0000 chunk 27 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 12 optimal weight: 0.3980 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.135634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.121973 restraints weight = 3625.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.125027 restraints weight = 1872.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.127164 restraints weight = 1126.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.128440 restraints weight = 749.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.129556 restraints weight = 557.442| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 2151 Z= 0.122 Angle : 0.554 6.717 2951 Z= 0.291 Chirality : 0.040 0.132 354 Planarity : 0.004 0.040 363 Dihedral : 3.813 15.554 312 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.15 % Allowed : 20.21 % Favored : 75.65 % 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: 2.39 (0.51), residues: 277 helix: 2.18 (0.35), residues: 226 sheet: None (None), residues: 0 loop : -1.26 (0.74), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 228 TYR 0.011 0.001 TYR R 308 PHE 0.014 0.001 PHE R 104 TRP 0.009 0.001 TRP R 109 HIS 0.001 0.000 HIS R 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 ( 2151) covalent geometry : angle 0.55418 / 0.29 ( 2951) hydrogen bonds : bond 0.04846 / 3.49 ( 160) hydrogen bonds : angle 3.56492 / 2.82 ( 480) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.082 Fit side-chains REVERT: R 318 ASN cc_start: 0.8534 (t0) cc_final: 0.8332 (t0) outliers start: 8 outliers final: 7 residues processed: 34 average time/residue: 0.0586 time to fit residues: 2.4097 Evaluate side-chains 36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 279 MET Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 3 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3441 r_free = 0.3441 target = 0.127414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.114518 restraints weight = 3814.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.117238 restraints weight = 2059.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.119175 restraints weight = 1275.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.120549 restraints weight = 870.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.121458 restraints weight = 639.900| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2151 Z= 0.137 Angle : 0.573 6.756 2951 Z= 0.302 Chirality : 0.040 0.134 354 Planarity : 0.004 0.039 363 Dihedral : 3.908 15.596 312 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.15 % Allowed : 20.21 % Favored : 75.65 % 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: 2.24 (0.50), residues: 277 helix: 2.09 (0.35), residues: 226 sheet: None (None), residues: 0 loop : -1.33 (0.73), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 228 TYR 0.012 0.001 TYR R 308 PHE 0.012 0.001 PHE R 104 TRP 0.006 0.001 TRP R 109 HIS 0.001 0.001 HIS R 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 ( 2151) covalent geometry : angle 0.57281 / 0.30 ( 2951) hydrogen bonds : bond 0.05329 / 3.86 ( 160) hydrogen bonds : angle 3.65520 / 2.88 ( 480) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.077 Fit side-chains REVERT: R 318 ASN cc_start: 0.8570 (t0) cc_final: 0.8349 (t0) REVERT: R 339 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8169 (mm) outliers start: 8 outliers final: 7 residues processed: 34 average time/residue: 0.0589 time to fit residues: 2.4043 Evaluate side-chains 37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 279 MET Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 0.0670 chunk 22 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 0.1980 chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 = 0.3446 r_free = 0.3446 target = 0.127587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.114683 restraints weight = 3884.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.117485 restraints weight = 2094.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.119429 restraints weight = 1291.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.120827 restraints weight = 882.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.121790 restraints weight = 647.973| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2151 Z= 0.130 Angle : 0.575 7.100 2951 Z= 0.303 Chirality : 0.040 0.131 354 Planarity : 0.004 0.039 363 Dihedral : 3.859 15.561 312 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.15 % Allowed : 20.21 % Favored : 75.65 % 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: 2.33 (0.51), residues: 277 helix: 2.12 (0.35), residues: 226 sheet: None (None), residues: 0 loop : -1.16 (0.78), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 228 TYR 0.012 0.001 TYR R 308 PHE 0.012 0.001 PHE R 104 TRP 0.008 0.001 TRP R 109 HIS 0.001 0.001 HIS R 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 ( 2151) covalent geometry : angle 0.57457 / 0.30 ( 2951) hydrogen bonds : bond 0.05136 / 3.71 ( 160) hydrogen bonds : angle 3.61942 / 2.86 ( 480) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.053 Fit side-chains REVERT: R 318 ASN cc_start: 0.8568 (t0) cc_final: 0.8340 (t0) REVERT: R 339 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8127 (mm) outliers start: 8 outliers final: 7 residues processed: 34 average time/residue: 0.0518 time to fit residues: 2.1253 Evaluate side-chains 37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 279 MET Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 7 optimal weight: 0.1980 chunk 22 optimal weight: 0.6980 chunk 27 optimal weight: 0.0570 chunk 17 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 overall best weight: 0.4498 ------------------------------------------------------------------------------- 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 = 0.3457 r_free = 0.3457 target = 0.128469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.115735 restraints weight = 3858.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.118538 restraints weight = 2075.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.120553 restraints weight = 1275.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.121813 restraints weight = 867.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.122756 restraints weight = 641.200| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2151 Z= 0.127 Angle : 0.568 6.895 2951 Z= 0.299 Chirality : 0.040 0.132 354 Planarity : 0.004 0.039 363 Dihedral : 3.822 15.554 312 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.15 % Allowed : 20.73 % Favored : 75.13 % 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: 2.39 (0.51), residues: 277 helix: 2.16 (0.35), residues: 226 sheet: None (None), residues: 0 loop : -1.11 (0.81), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 228 TYR 0.011 0.001 TYR R 308 PHE 0.012 0.001 PHE R 104 TRP 0.007 0.001 TRP R 109 HIS 0.001 0.001 HIS R 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 ( 2151) covalent geometry : angle 0.56847 / 0.30 ( 2951) hydrogen bonds : bond 0.04967 / 3.59 ( 160) hydrogen bonds : angle 3.59814 / 2.84 ( 480) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 650.83 seconds wall clock time: 11 minutes 48.36 seconds (708.36 seconds total)