Starting phenix.real_space_refine on Tue Mar 3 12:44:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8csy_26975/03_2026/8csy_26975.cif Found real_map, /net/cci-nas-00/data/ceres_data/8csy_26975/03_2026/8csy_26975.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8csy_26975/03_2026/8csy_26975.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8csy_26975/03_2026/8csy_26975.map" model { file = "/net/cci-nas-00/data/ceres_data/8csy_26975/03_2026/8csy_26975.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8csy_26975/03_2026/8csy_26975.cif" } resolution = 2.7 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= 0.001 sd= 0.291 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 12 5.16 5 C 2941 2.51 5 N 805 2.21 5 O 880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4638 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 2276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2276 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 267} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 2343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2343 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 280} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Time building chain proxies: 1.03, per 1000 atoms: 0.22 Number of scatterers: 4638 At special positions: 0 Unit cell: (89.64, 83, 74.285, 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 12 16.00 O 880 8.00 N 805 7.00 C 2941 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: 0.28 Conformation dependent library (CDL) restraints added in 340.7 milliseconds 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1108 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 4 sheets defined 40.1% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'E' and resid 104 through 116 removed outlier: 3.834A pdb=" N LYS E 116 " --> pdb=" O ARG E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 142 Processing helix chain 'E' and resid 146 through 148 No H-bonds generated for 'chain 'E' and resid 146 through 148' Processing helix chain 'E' and resid 149 through 158 Processing helix chain 'E' and resid 163 through 167 Processing helix chain 'E' and resid 194 through 201 Processing helix chain 'E' and resid 277 through 291 Processing helix chain 'E' and resid 291 through 301 Processing helix chain 'E' and resid 303 through 317 removed outlier: 3.730A pdb=" N LEU E 307 " --> pdb=" O SER E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 333 Processing helix chain 'E' and resid 335 through 348 Processing helix chain 'C' and resid 42 through 47 removed outlier: 3.532A pdb=" N HIS C 47 " --> pdb=" O THR C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 116 removed outlier: 3.688A pdb=" N LYS C 116 " --> pdb=" O ARG C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 149 through 158 Processing helix chain 'C' and resid 163 through 167 Processing helix chain 'C' and resid 194 through 201 Processing helix chain 'C' and resid 277 through 291 Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 303 through 317 removed outlier: 3.689A pdb=" N LEU C 307 " --> pdb=" O SER C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 334 Processing helix chain 'C' and resid 334 through 343 removed outlier: 4.268A pdb=" N VAL C 338 " --> pdb=" O SER C 334 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 58 through 67 removed outlier: 6.017A pdb=" N GLU E 63 " --> pdb=" O GLU E 77 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLU E 77 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL E 65 " --> pdb=" O TRP E 75 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N TRP E 75 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASP E 67 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU E 73 " --> pdb=" O ASP E 67 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 85 through 87 current: chain 'E' and resid 262 through 270 Processing sheet with id=AA2, first strand: chain 'E' and resid 102 through 103 Processing sheet with id=AA3, first strand: chain 'E' and resid 177 through 178 Processing sheet with id=AA4, first strand: chain 'C' and resid 56 through 66 removed outlier: 6.584A pdb=" N VAL C 59 " --> pdb=" O ARG C 80 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ARG C 80 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU C 61 " --> pdb=" O ALA C 78 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 85 through 87 current: chain 'C' and resid 224 through 234 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 224 through 234 current: chain 'C' and resid 262 through 270 165 hydrogen bonds defined for protein. 465 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: 0.54 Time building geometry restraints manager: 0.42 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: 1575 1.34 - 1.46: 781 1.46 - 1.57: 2337 1.57 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 4713 Sorted by residual: bond pdb=" C VAL E 336 " pdb=" N PRO E 337 " ideal model delta sigma weight residual 1.335 1.346 -0.011 1.28e-02 6.10e+03 7.71e-01 bond pdb=" C VAL C 336 " pdb=" N PRO C 337 " ideal model delta sigma weight residual 1.336 1.346 -0.011 1.23e-02 6.61e+03 7.66e-01 bond pdb=" C PRO C 221 " pdb=" N PRO C 222 " ideal model delta sigma weight residual 1.335 1.344 -0.009 1.30e-02 5.92e+03 4.91e-01 bond pdb=" CA PRO C 271 " pdb=" C PRO C 271 " ideal model delta sigma weight residual 1.525 1.519 0.007 9.70e-03 1.06e+04 4.61e-01 bond pdb=" N ASP E 122 " pdb=" CA ASP E 122 " ideal model delta sigma weight residual 1.460 1.469 -0.010 1.42e-02 4.96e+03 4.56e-01 ... (remaining 4708 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 6213 1.36 - 2.71: 155 2.71 - 4.07: 27 4.07 - 5.42: 6 5.42 - 6.78: 4 Bond angle restraints: 6405 Sorted by residual: angle pdb=" N ASN C 91 " pdb=" CA ASN C 91 " pdb=" C ASN C 91 " ideal model delta sigma weight residual 114.09 108.87 5.22 1.55e+00 4.16e-01 1.13e+01 angle pdb=" C VAL E 82 " pdb=" N GLN E 83 " pdb=" CA GLN E 83 " ideal model delta sigma weight residual 121.54 127.29 -5.75 1.91e+00 2.74e-01 9.06e+00 angle pdb=" N GLU C 90 " pdb=" CA GLU C 90 " pdb=" C GLU C 90 " ideal model delta sigma weight residual 111.81 108.25 3.56 1.44e+00 4.82e-01 6.10e+00 angle pdb=" N VAL E 82 " pdb=" CA VAL E 82 " pdb=" C VAL E 82 " ideal model delta sigma weight residual 109.34 104.62 4.72 2.08e+00 2.31e-01 5.15e+00 angle pdb=" CA PRO C 271 " pdb=" C PRO C 271 " pdb=" N GLU C 272 " ideal model delta sigma weight residual 114.74 116.96 -2.22 1.03e+00 9.43e-01 4.64e+00 ... (remaining 6400 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.74: 2624 16.74 - 33.47: 149 33.47 - 50.21: 70 50.21 - 66.94: 23 66.94 - 83.68: 5 Dihedral angle restraints: 2871 sinusoidal: 1175 harmonic: 1696 Sorted by residual: dihedral pdb=" CA TRP E 81 " pdb=" C TRP E 81 " pdb=" N VAL E 82 " pdb=" CA VAL E 82 " ideal model delta harmonic sigma weight residual 180.00 155.74 24.26 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA VAL C 57 " pdb=" C VAL C 57 " pdb=" N TYR C 58 " pdb=" CA TYR C 58 " ideal model delta harmonic sigma weight residual 180.00 162.18 17.82 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CB GLU E 312 " pdb=" CG GLU E 312 " pdb=" CD GLU E 312 " pdb=" OE1 GLU E 312 " ideal model delta sinusoidal sigma weight residual 0.00 83.68 -83.68 1 3.00e+01 1.11e-03 9.49e+00 ... (remaining 2868 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 441 0.029 - 0.057: 187 0.057 - 0.085: 71 0.085 - 0.114: 31 0.114 - 0.142: 3 Chirality restraints: 733 Sorted by residual: chirality pdb=" CA VAL E 82 " pdb=" N VAL E 82 " pdb=" C VAL E 82 " pdb=" CB VAL E 82 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CA ILE E 220 " pdb=" N ILE E 220 " pdb=" C ILE E 220 " pdb=" CB ILE E 220 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.50e-01 chirality pdb=" CA VAL C 82 " pdb=" N VAL C 82 " pdb=" C VAL C 82 " pdb=" CB VAL C 82 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.28e-01 ... (remaining 730 not shown) Planarity restraints: 840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 146 " -0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO C 147 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 147 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 147 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 183 " -0.023 5.00e-02 4.00e+02 3.49e-02 1.94e+00 pdb=" N PRO E 184 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO E 184 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 184 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 146 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO E 147 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO E 147 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 147 " -0.018 5.00e-02 4.00e+02 ... (remaining 837 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 688 2.76 - 3.29: 4203 3.29 - 3.83: 8186 3.83 - 4.36: 9643 4.36 - 4.90: 16030 Nonbonded interactions: 38750 Sorted by model distance: nonbonded pdb=" OG1 THR C 103 " pdb=" OG SER C 106 " model vdw 2.224 3.040 nonbonded pdb=" NH2 ARG E 292 " pdb=" O LYS E 353 " model vdw 2.304 3.120 nonbonded pdb=" OD1 ASP E 316 " pdb=" NE1 TRP C 105 " model vdw 2.305 3.120 nonbonded pdb=" O ALA E 331 " pdb=" OG SER E 334 " model vdw 2.310 3.040 nonbonded pdb=" OD2 ASP C 122 " pdb=" O HOH C1001 " model vdw 2.328 3.040 ... (remaining 38745 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 'C' and (resid 56 through 203 or resid 217 through 348)) selection = (chain 'E' and ((resid 56 and (name N or name CA or name C or name O or name CB \ )) or resid 57 through 181 or resid 192 through 348)) } 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: 1.540 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: 0.330 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.180 Find NCS groups from input model: 0.080 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:10.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 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 : 0.003 0.033 4713 Z= 0.140 Angle : 0.559 6.781 6405 Z= 0.303 Chirality : 0.038 0.142 733 Planarity : 0.005 0.038 840 Dihedral : 14.356 83.678 1763 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 4.06 % Allowed : 8.72 % Favored : 87.22 % 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: 1.07 (0.34), residues: 574 helix: 1.13 (0.36), residues: 212 sheet: 2.27 (0.52), residues: 89 loop : -0.10 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 304 TYR 0.009 0.001 TYR E 278 PHE 0.020 0.002 PHE C 314 TRP 0.009 0.001 TRP E 81 HIS 0.003 0.001 HIS E 101 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 4713) covalent geometry : angle 0.55937 ( 6405) hydrogen bonds : bond 0.13705 ( 165) hydrogen bonds : angle 5.65196 ( 465) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 69 LYS cc_start: 0.6575 (OUTLIER) cc_final: 0.5567 (ptpt) REVERT: E 112 ARG cc_start: 0.7610 (ttm-80) cc_final: 0.7350 (ttp-170) REVERT: E 125 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7840 (mm-30) REVERT: E 233 ARG cc_start: 0.8376 (mtm180) cc_final: 0.8161 (mtm180) REVERT: E 291 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8683 (tm-30) REVERT: E 348 GLN cc_start: 0.7370 (pt0) cc_final: 0.7160 (pt0) REVERT: C 83 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.7345 (pm20) REVERT: C 109 GLU cc_start: 0.7684 (tp30) cc_final: 0.7363 (mp0) REVERT: C 124 GLN cc_start: 0.8432 (mt0) cc_final: 0.7772 (tm-30) REVERT: C 198 GLN cc_start: 0.7841 (tt0) cc_final: 0.7400 (mt0) REVERT: C 300 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7721 (mmm) outliers start: 20 outliers final: 3 residues processed: 123 average time/residue: 0.7217 time to fit residues: 91.3620 Evaluate side-chains 103 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 300 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 54 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 83 GLN C 144 GLN C 239 GLN C 248 GLN C 339 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.148189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.118638 restraints weight = 4978.044| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.86 r_work: 0.3047 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4713 Z= 0.144 Angle : 0.539 5.801 6405 Z= 0.273 Chirality : 0.039 0.131 733 Planarity : 0.004 0.035 840 Dihedral : 7.010 58.331 647 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.26 % Allowed : 12.37 % Favored : 83.37 % 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: 1.19 (0.34), residues: 574 helix: 1.36 (0.36), residues: 219 sheet: 2.00 (0.52), residues: 90 loop : -0.08 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 138 TYR 0.010 0.002 TYR E 278 PHE 0.020 0.002 PHE C 314 TRP 0.013 0.002 TRP E 81 HIS 0.002 0.001 HIS E 309 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 4713) covalent geometry : angle 0.53898 ( 6405) hydrogen bonds : bond 0.04395 ( 165) hydrogen bonds : angle 4.44416 ( 465) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: E 69 LYS cc_start: 0.6712 (OUTLIER) cc_final: 0.5747 (ptpt) REVERT: E 109 GLU cc_start: 0.8201 (tp30) cc_final: 0.7881 (tp30) REVERT: E 112 ARG cc_start: 0.7940 (ttm-80) cc_final: 0.7302 (ttp-170) REVERT: E 125 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7879 (mm-30) REVERT: E 158 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8397 (mm) REVERT: E 219 LYS cc_start: 0.7174 (OUTLIER) cc_final: 0.5538 (pmtt) REVERT: E 348 GLN cc_start: 0.7619 (pt0) cc_final: 0.7280 (pt0) REVERT: C 83 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7518 (pm20) REVERT: C 109 GLU cc_start: 0.7858 (tp30) cc_final: 0.7381 (mm-30) REVERT: C 114 PHE cc_start: 0.8476 (OUTLIER) cc_final: 0.7825 (t80) REVERT: C 124 GLN cc_start: 0.8715 (mt0) cc_final: 0.7807 (tm-30) REVERT: C 198 GLN cc_start: 0.7858 (tt0) cc_final: 0.7330 (mt0) REVERT: C 202 GLU cc_start: 0.4317 (OUTLIER) cc_final: 0.3750 (tp30) REVERT: C 233 ARG cc_start: 0.8212 (mtt-85) cc_final: 0.7913 (mpp80) REVERT: C 272 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7165 (mm-30) REVERT: C 300 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.7963 (mmm) REVERT: C 330 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7339 (tt0) outliers start: 21 outliers final: 7 residues processed: 99 average time/residue: 0.7106 time to fit residues: 72.3816 Evaluate side-chains 102 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 332 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 5 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 6 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.147454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.117985 restraints weight = 4953.006| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.83 r_work: 0.3038 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4713 Z= 0.165 Angle : 0.548 6.014 6405 Z= 0.276 Chirality : 0.040 0.124 733 Planarity : 0.004 0.035 840 Dihedral : 6.484 54.068 644 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.06 % Allowed : 13.79 % Favored : 82.15 % 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: 1.02 (0.34), residues: 574 helix: 1.31 (0.36), residues: 219 sheet: 2.10 (0.57), residues: 78 loop : -0.21 (0.34), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 138 TYR 0.011 0.002 TYR E 278 PHE 0.021 0.002 PHE C 314 TRP 0.014 0.002 TRP E 81 HIS 0.003 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 4713) covalent geometry : angle 0.54782 ( 6405) hydrogen bonds : bond 0.04387 ( 165) hydrogen bonds : angle 4.38227 ( 465) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: E 69 LYS cc_start: 0.6780 (OUTLIER) cc_final: 0.5854 (ptpt) REVERT: E 112 ARG cc_start: 0.7947 (ttm-80) cc_final: 0.7349 (ttp-170) REVERT: E 125 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7953 (mm-30) REVERT: E 158 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8403 (mm) REVERT: E 198 GLN cc_start: 0.6965 (mt0) cc_final: 0.6308 (tp40) REVERT: E 219 LYS cc_start: 0.7250 (OUTLIER) cc_final: 0.5527 (pmtt) REVERT: E 348 GLN cc_start: 0.7661 (pt0) cc_final: 0.7279 (pt0) REVERT: C 83 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7537 (pm20) REVERT: C 109 GLU cc_start: 0.7856 (tp30) cc_final: 0.7459 (mm-30) REVERT: C 114 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.7834 (t80) REVERT: C 124 GLN cc_start: 0.8712 (mt0) cc_final: 0.7815 (tm-30) REVERT: C 202 GLU cc_start: 0.4348 (OUTLIER) cc_final: 0.3787 (tp30) REVERT: C 216 ILE cc_start: 0.5868 (OUTLIER) cc_final: 0.5381 (tp) REVERT: C 272 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7234 (mm-30) REVERT: C 300 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.7961 (mmm) REVERT: C 330 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7313 (tt0) outliers start: 20 outliers final: 5 residues processed: 100 average time/residue: 0.6890 time to fit residues: 70.9617 Evaluate side-chains 100 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 330 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 50 optimal weight: 0.0980 chunk 14 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.146240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.116638 restraints weight = 4953.693| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.84 r_work: 0.3025 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4713 Z= 0.194 Angle : 0.576 6.117 6405 Z= 0.290 Chirality : 0.041 0.121 733 Planarity : 0.005 0.036 840 Dihedral : 6.547 52.545 644 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 5.07 % Allowed : 13.79 % Favored : 81.14 % 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: 0.91 (0.34), residues: 574 helix: 1.27 (0.36), residues: 218 sheet: 1.97 (0.57), residues: 78 loop : -0.29 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 304 TYR 0.011 0.002 TYR C 278 PHE 0.022 0.002 PHE C 314 TRP 0.014 0.002 TRP E 81 HIS 0.004 0.001 HIS C 163 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 4713) covalent geometry : angle 0.57586 ( 6405) hydrogen bonds : bond 0.04520 ( 165) hydrogen bonds : angle 4.38923 ( 465) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: E 60 GLU cc_start: 0.8884 (tt0) cc_final: 0.8653 (tt0) REVERT: E 69 LYS cc_start: 0.6878 (OUTLIER) cc_final: 0.5919 (ptpt) REVERT: E 112 ARG cc_start: 0.7957 (ttm-80) cc_final: 0.7339 (ttp-170) REVERT: E 125 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7940 (mm-30) REVERT: E 198 GLN cc_start: 0.6976 (mt0) cc_final: 0.6323 (tp40) REVERT: E 219 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.5563 (pmtt) REVERT: E 348 GLN cc_start: 0.7677 (pt0) cc_final: 0.7286 (pt0) REVERT: C 109 GLU cc_start: 0.7898 (tp30) cc_final: 0.7467 (mm-30) REVERT: C 114 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.7829 (t80) REVERT: C 124 GLN cc_start: 0.8701 (mt0) cc_final: 0.7808 (tm-30) REVERT: C 202 GLU cc_start: 0.4398 (OUTLIER) cc_final: 0.3854 (tp30) REVERT: C 216 ILE cc_start: 0.5878 (OUTLIER) cc_final: 0.5318 (tp) REVERT: C 252 GLU cc_start: 0.8370 (mm-30) cc_final: 0.7979 (mt-10) REVERT: C 272 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7268 (mm-30) REVERT: C 300 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.7972 (mmm) REVERT: C 330 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7341 (tt0) outliers start: 25 outliers final: 5 residues processed: 103 average time/residue: 0.6987 time to fit residues: 74.2136 Evaluate side-chains 96 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 330 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 38 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 13 optimal weight: 30.0000 chunk 16 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 0 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.146883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.117278 restraints weight = 4953.842| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.84 r_work: 0.3034 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4713 Z= 0.156 Angle : 0.540 5.951 6405 Z= 0.272 Chirality : 0.039 0.120 733 Planarity : 0.004 0.035 840 Dihedral : 6.305 52.140 641 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.46 % Allowed : 14.81 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.34), residues: 574 helix: 1.32 (0.37), residues: 218 sheet: 1.90 (0.57), residues: 78 loop : -0.25 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 138 TYR 0.011 0.002 TYR C 278 PHE 0.021 0.002 PHE C 314 TRP 0.014 0.002 TRP E 81 HIS 0.003 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 4713) covalent geometry : angle 0.53959 ( 6405) hydrogen bonds : bond 0.04184 ( 165) hydrogen bonds : angle 4.35036 ( 465) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: E 60 GLU cc_start: 0.8889 (tt0) cc_final: 0.8673 (tt0) REVERT: E 69 LYS cc_start: 0.6890 (OUTLIER) cc_final: 0.5888 (ptpt) REVERT: E 112 ARG cc_start: 0.7953 (ttm-80) cc_final: 0.7351 (ttp-170) REVERT: E 125 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7927 (mm-30) REVERT: E 158 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8411 (mm) REVERT: E 219 LYS cc_start: 0.7291 (OUTLIER) cc_final: 0.5543 (pmtt) REVERT: E 348 GLN cc_start: 0.7674 (pt0) cc_final: 0.7270 (pt0) REVERT: C 83 GLN cc_start: 0.7917 (pt0) cc_final: 0.7565 (pm20) REVERT: C 109 GLU cc_start: 0.7877 (tp30) cc_final: 0.7482 (mm-30) REVERT: C 114 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.7898 (t80) REVERT: C 124 GLN cc_start: 0.8717 (mt0) cc_final: 0.7824 (tm-30) REVERT: C 198 GLN cc_start: 0.7862 (tt0) cc_final: 0.7162 (mt0) REVERT: C 202 GLU cc_start: 0.4370 (OUTLIER) cc_final: 0.3831 (tp30) REVERT: C 216 ILE cc_start: 0.5857 (OUTLIER) cc_final: 0.5283 (tp) REVERT: C 233 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7160 (mtt-85) REVERT: C 252 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7982 (mt-10) REVERT: C 272 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7233 (mm-30) REVERT: C 300 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.7983 (mmm) REVERT: C 328 SER cc_start: 0.7966 (m) cc_final: 0.7653 (t) REVERT: C 330 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7339 (tt0) outliers start: 22 outliers final: 4 residues processed: 98 average time/residue: 0.6683 time to fit residues: 67.5831 Evaluate side-chains 100 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 ARG Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 330 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 11 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 134 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.147360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.117963 restraints weight = 5005.258| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.84 r_work: 0.3021 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4713 Z= 0.148 Angle : 0.528 5.749 6405 Z= 0.267 Chirality : 0.039 0.119 733 Planarity : 0.004 0.034 840 Dihedral : 6.232 51.881 641 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.06 % Allowed : 16.43 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.34), residues: 574 helix: 1.36 (0.37), residues: 218 sheet: 1.81 (0.57), residues: 78 loop : -0.25 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 138 TYR 0.011 0.002 TYR E 278 PHE 0.021 0.002 PHE C 314 TRP 0.014 0.002 TRP E 81 HIS 0.004 0.001 HIS C 163 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 4713) covalent geometry : angle 0.52841 ( 6405) hydrogen bonds : bond 0.04059 ( 165) hydrogen bonds : angle 4.31225 ( 465) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: E 60 GLU cc_start: 0.8890 (tt0) cc_final: 0.8682 (tt0) REVERT: E 69 LYS cc_start: 0.6884 (OUTLIER) cc_final: 0.5892 (ptpt) REVERT: E 83 GLN cc_start: 0.8060 (tp-100) cc_final: 0.7791 (mm-40) REVERT: E 112 ARG cc_start: 0.7952 (ttm-80) cc_final: 0.7315 (ttp-170) REVERT: E 125 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7931 (mm-30) REVERT: E 158 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8402 (mm) REVERT: E 219 LYS cc_start: 0.7268 (OUTLIER) cc_final: 0.5634 (pmtt) REVERT: E 348 GLN cc_start: 0.7670 (pt0) cc_final: 0.7250 (pt0) REVERT: C 83 GLN cc_start: 0.7930 (pt0) cc_final: 0.7564 (pm20) REVERT: C 109 GLU cc_start: 0.7887 (tp30) cc_final: 0.7422 (mm-30) REVERT: C 114 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.7876 (t80) REVERT: C 124 GLN cc_start: 0.8759 (mt0) cc_final: 0.7814 (tm-30) REVERT: C 198 GLN cc_start: 0.7862 (tt0) cc_final: 0.7044 (mm110) REVERT: C 202 GLU cc_start: 0.4377 (OUTLIER) cc_final: 0.3832 (tp30) REVERT: C 216 ILE cc_start: 0.5800 (OUTLIER) cc_final: 0.5254 (tp) REVERT: C 233 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7198 (mtt-85) REVERT: C 272 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7285 (mm-30) REVERT: C 300 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.7983 (mmm) REVERT: C 328 SER cc_start: 0.7978 (m) cc_final: 0.7646 (t) REVERT: C 330 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7341 (tt0) outliers start: 20 outliers final: 4 residues processed: 99 average time/residue: 0.6940 time to fit residues: 70.8460 Evaluate side-chains 99 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 ARG Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 330 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 16 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 11 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.146827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.117536 restraints weight = 4935.533| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.83 r_work: 0.3035 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4713 Z= 0.166 Angle : 0.554 5.838 6405 Z= 0.279 Chirality : 0.040 0.119 733 Planarity : 0.004 0.034 840 Dihedral : 6.297 52.483 641 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.06 % Allowed : 16.84 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.34), residues: 574 helix: 1.32 (0.37), residues: 218 sheet: 1.77 (0.57), residues: 78 loop : -0.29 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 138 TYR 0.011 0.002 TYR C 278 PHE 0.021 0.002 PHE C 314 TRP 0.014 0.002 TRP E 81 HIS 0.004 0.001 HIS C 163 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 4713) covalent geometry : angle 0.55408 ( 6405) hydrogen bonds : bond 0.04245 ( 165) hydrogen bonds : angle 4.31234 ( 465) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: E 60 GLU cc_start: 0.8886 (tt0) cc_final: 0.8673 (tt0) REVERT: E 69 LYS cc_start: 0.6903 (OUTLIER) cc_final: 0.5909 (ptpt) REVERT: E 83 GLN cc_start: 0.8057 (tp-100) cc_final: 0.7805 (mm-40) REVERT: E 112 ARG cc_start: 0.7958 (ttm-80) cc_final: 0.7349 (ttp-170) REVERT: E 125 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7918 (mm-30) REVERT: E 158 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8430 (mm) REVERT: E 198 GLN cc_start: 0.6949 (mt0) cc_final: 0.6280 (tp40) REVERT: E 219 LYS cc_start: 0.7310 (OUTLIER) cc_final: 0.5643 (pmtt) REVERT: E 348 GLN cc_start: 0.7669 (pt0) cc_final: 0.7242 (pt0) REVERT: C 83 GLN cc_start: 0.7930 (pt0) cc_final: 0.7578 (pm20) REVERT: C 109 GLU cc_start: 0.7895 (tp30) cc_final: 0.7421 (mm-30) REVERT: C 114 PHE cc_start: 0.8486 (OUTLIER) cc_final: 0.7910 (t80) REVERT: C 124 GLN cc_start: 0.8714 (mt0) cc_final: 0.7813 (tm-30) REVERT: C 202 GLU cc_start: 0.4395 (OUTLIER) cc_final: 0.3871 (tp30) REVERT: C 216 ILE cc_start: 0.5837 (OUTLIER) cc_final: 0.5262 (tp) REVERT: C 233 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7235 (mtt-85) REVERT: C 252 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7988 (mt-10) REVERT: C 300 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.7962 (mmm) REVERT: C 328 SER cc_start: 0.7990 (m) cc_final: 0.7666 (t) REVERT: C 330 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7379 (tt0) outliers start: 20 outliers final: 4 residues processed: 98 average time/residue: 0.7040 time to fit residues: 71.1583 Evaluate side-chains 98 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 ARG Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 330 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 25 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 47 optimal weight: 7.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.148619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.119213 restraints weight = 5036.231| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.86 r_work: 0.3065 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4713 Z= 0.112 Angle : 0.496 5.453 6405 Z= 0.249 Chirality : 0.038 0.118 733 Planarity : 0.004 0.033 840 Dihedral : 6.083 52.236 641 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 4.06 % Allowed : 17.44 % Favored : 78.50 % 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: 1.07 (0.35), residues: 574 helix: 1.46 (0.37), residues: 219 sheet: 1.64 (0.57), residues: 83 loop : -0.17 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 138 TYR 0.009 0.001 TYR E 278 PHE 0.019 0.002 PHE C 314 TRP 0.015 0.001 TRP E 81 HIS 0.003 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 4713) covalent geometry : angle 0.49611 ( 6405) hydrogen bonds : bond 0.03610 ( 165) hydrogen bonds : angle 4.27880 ( 465) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: E 60 GLU cc_start: 0.8870 (tt0) cc_final: 0.8667 (tt0) REVERT: E 69 LYS cc_start: 0.6850 (OUTLIER) cc_final: 0.5823 (ptpt) REVERT: E 112 ARG cc_start: 0.7959 (ttm-80) cc_final: 0.7340 (ttp-170) REVERT: E 125 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7907 (mm-30) REVERT: E 158 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8354 (mm) REVERT: E 219 LYS cc_start: 0.7259 (OUTLIER) cc_final: 0.5593 (pmtt) REVERT: E 291 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.7923 (tm-30) REVERT: E 348 GLN cc_start: 0.7573 (pt0) cc_final: 0.7156 (pt0) REVERT: C 83 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7516 (pm20) REVERT: C 109 GLU cc_start: 0.7869 (tp30) cc_final: 0.7316 (mm-30) REVERT: C 114 PHE cc_start: 0.8465 (OUTLIER) cc_final: 0.7891 (t80) REVERT: C 124 GLN cc_start: 0.8701 (mt0) cc_final: 0.7803 (tm-30) REVERT: C 202 GLU cc_start: 0.4334 (OUTLIER) cc_final: 0.3818 (tp30) REVERT: C 216 ILE cc_start: 0.5762 (OUTLIER) cc_final: 0.5189 (tp) REVERT: C 233 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7204 (mtt-85) REVERT: C 252 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8012 (mt-10) REVERT: C 300 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.7920 (mmm) REVERT: C 328 SER cc_start: 0.7940 (m) cc_final: 0.7661 (t) REVERT: C 330 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7349 (tt0) outliers start: 20 outliers final: 5 residues processed: 102 average time/residue: 0.6727 time to fit residues: 70.7494 Evaluate side-chains 104 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 ARG Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 330 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 GLN C 239 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.146235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.116687 restraints weight = 4920.365| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.84 r_work: 0.3030 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4713 Z= 0.191 Angle : 0.578 5.872 6405 Z= 0.289 Chirality : 0.041 0.145 733 Planarity : 0.004 0.034 840 Dihedral : 6.313 52.985 641 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.85 % Allowed : 18.05 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.34), residues: 574 helix: 1.34 (0.37), residues: 218 sheet: 1.65 (0.57), residues: 78 loop : -0.26 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 138 TYR 0.014 0.002 TYR E 278 PHE 0.022 0.002 PHE C 314 TRP 0.013 0.002 TRP E 81 HIS 0.005 0.001 HIS C 163 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 4713) covalent geometry : angle 0.57847 ( 6405) hydrogen bonds : bond 0.04400 ( 165) hydrogen bonds : angle 4.32082 ( 465) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: E 60 GLU cc_start: 0.8890 (tt0) cc_final: 0.8659 (tt0) REVERT: E 69 LYS cc_start: 0.6916 (OUTLIER) cc_final: 0.5977 (ptpt) REVERT: E 83 GLN cc_start: 0.8083 (tp-100) cc_final: 0.7873 (mm-40) REVERT: E 112 ARG cc_start: 0.7968 (ttm-80) cc_final: 0.7348 (ttp-170) REVERT: E 125 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7911 (mm-30) REVERT: E 198 GLN cc_start: 0.6942 (mt0) cc_final: 0.6283 (tp40) REVERT: E 219 LYS cc_start: 0.7333 (OUTLIER) cc_final: 0.5645 (pmtt) REVERT: E 348 GLN cc_start: 0.7702 (pt0) cc_final: 0.7264 (pt0) REVERT: C 83 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7583 (pm20) REVERT: C 109 GLU cc_start: 0.7951 (tp30) cc_final: 0.7388 (mm-30) REVERT: C 114 PHE cc_start: 0.8494 (OUTLIER) cc_final: 0.7840 (t80) REVERT: C 124 GLN cc_start: 0.8732 (mt0) cc_final: 0.7813 (tm-30) REVERT: C 155 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7998 (ttp-110) REVERT: C 202 GLU cc_start: 0.4427 (OUTLIER) cc_final: 0.3890 (tp30) REVERT: C 216 ILE cc_start: 0.5815 (OUTLIER) cc_final: 0.5248 (tp) REVERT: C 233 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7261 (mtt-85) REVERT: C 252 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8007 (mt-10) REVERT: C 300 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.7967 (mmm) REVERT: C 330 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7363 (tt0) outliers start: 19 outliers final: 6 residues processed: 94 average time/residue: 0.7073 time to fit residues: 68.4361 Evaluate side-chains 100 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 155 ARG Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 ARG Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 330 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 30 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 32 optimal weight: 8.9990 chunk 42 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 2 optimal weight: 7.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.147097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.117666 restraints weight = 4964.848| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.84 r_work: 0.3043 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4713 Z= 0.154 Angle : 0.544 5.691 6405 Z= 0.273 Chirality : 0.039 0.124 733 Planarity : 0.004 0.034 840 Dihedral : 6.253 52.692 641 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.65 % Allowed : 18.46 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.34), residues: 574 helix: 1.32 (0.37), residues: 219 sheet: 1.61 (0.57), residues: 78 loop : -0.23 (0.34), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 138 TYR 0.014 0.002 TYR E 278 PHE 0.021 0.002 PHE C 314 TRP 0.013 0.002 TRP E 81 HIS 0.004 0.001 HIS C 163 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 4713) covalent geometry : angle 0.54401 ( 6405) hydrogen bonds : bond 0.04077 ( 165) hydrogen bonds : angle 4.30039 ( 465) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: E 60 GLU cc_start: 0.8889 (tt0) cc_final: 0.8676 (tt0) REVERT: E 69 LYS cc_start: 0.6885 (OUTLIER) cc_final: 0.5907 (ptpt) REVERT: E 83 GLN cc_start: 0.8013 (tp-100) cc_final: 0.7801 (mm-40) REVERT: E 112 ARG cc_start: 0.7976 (ttm-80) cc_final: 0.7353 (ttp-170) REVERT: E 125 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7915 (mm-30) REVERT: E 158 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8402 (mm) REVERT: E 219 LYS cc_start: 0.7311 (OUTLIER) cc_final: 0.5630 (pmtt) REVERT: E 348 GLN cc_start: 0.7652 (pt0) cc_final: 0.7220 (pt0) REVERT: C 109 GLU cc_start: 0.7940 (tp30) cc_final: 0.7378 (mm-30) REVERT: C 114 PHE cc_start: 0.8487 (OUTLIER) cc_final: 0.7834 (t80) REVERT: C 124 GLN cc_start: 0.8728 (mt0) cc_final: 0.7803 (tm-30) REVERT: C 155 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7938 (ttp-110) REVERT: C 202 GLU cc_start: 0.4400 (OUTLIER) cc_final: 0.3879 (tp30) REVERT: C 216 ILE cc_start: 0.5786 (OUTLIER) cc_final: 0.5197 (tp) REVERT: C 233 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7291 (mtt-85) REVERT: C 252 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7999 (mt-10) REVERT: C 300 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.7960 (mmm) REVERT: C 330 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7349 (tt0) outliers start: 18 outliers final: 6 residues processed: 91 average time/residue: 0.7069 time to fit residues: 66.2960 Evaluate side-chains 100 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 155 ARG Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 ARG Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 330 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 13 optimal weight: 0.0980 chunk 41 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.148355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.118987 restraints weight = 4955.955| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.84 r_work: 0.3059 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4713 Z= 0.116 Angle : 0.503 5.485 6405 Z= 0.253 Chirality : 0.038 0.124 733 Planarity : 0.004 0.033 840 Dihedral : 6.102 52.138 641 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.25 % Allowed : 18.66 % Favored : 78.09 % 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: 1.03 (0.35), residues: 574 helix: 1.44 (0.37), residues: 219 sheet: 1.44 (0.57), residues: 83 loop : -0.13 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 138 TYR 0.014 0.002 TYR E 278 PHE 0.019 0.002 PHE C 314 TRP 0.015 0.001 TRP E 81 HIS 0.003 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 4713) covalent geometry : angle 0.50290 ( 6405) hydrogen bonds : bond 0.03660 ( 165) hydrogen bonds : angle 4.26631 ( 465) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2342.58 seconds wall clock time: 40 minutes 28.87 seconds (2428.87 seconds total)