Starting phenix.real_space_refine on Tue Feb 3 13:02:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ko6_62470/02_2026/9ko6_62470_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ko6_62470/02_2026/9ko6_62470.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ko6_62470/02_2026/9ko6_62470_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ko6_62470/02_2026/9ko6_62470_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ko6_62470/02_2026/9ko6_62470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ko6_62470/02_2026/9ko6_62470.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.039 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 20 5.16 5 C 1811 2.51 5 N 437 2.21 5 O 475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2743 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 450 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 6, 'TRANS': 62} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 6, 'ASN:plan1': 1, 'PHE:plan': 1, 'HIS:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 73 Chain: "R" Number of atoms: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2293 Classifications: {'peptide': 300} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 6, 'TRANS': 293} Chain breaks: 1 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 6, 'GLN:plan1': 2, 'GLU:plan': 1, 'PHE:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 81 Time building chain proxies: 0.84, per 1000 atoms: 0.31 Number of scatterers: 2743 At special positions: 0 Unit cell: (52.56, 71.54, 97.09, 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 20 16.00 O 475 8.00 N 437 7.00 C 1811 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS C 34 " distance=2.03 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 50 " distance=2.03 Simple disulfide: pdb=" SG CYS R 129 " - pdb=" SG CYS R 210 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.24 Conformation dependent library (CDL) restraints added in 111.2 milliseconds 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 710 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 1 sheets defined 70.2% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'C' and resid 55 through 67 removed outlier: 3.948A pdb=" N ARG C 67 " --> pdb=" O GLN C 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 87 Proline residue: R 62 - end of helix Processing helix chain 'R' and resid 91 through 120 removed outlier: 3.608A pdb=" N THR R 95 " --> pdb=" O THR R 91 " (cutoff:3.500A) Proline residue: R 112 - end of helix Processing helix chain 'R' and resid 125 through 159 removed outlier: 3.612A pdb=" N LYS R 137 " --> pdb=" O PHE R 133 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU R 148 " --> pdb=" O MET R 144 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 190 Processing helix chain 'R' and resid 190 through 196 Processing helix chain 'R' and resid 216 through 230 removed outlier: 4.169A pdb=" N PHE R 220 " --> pdb=" O HIS R 216 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 253 removed outlier: 3.518A pdb=" N VAL R 245 " --> pdb=" O PHE R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 290 removed outlier: 3.829A pdb=" N ILE R 262 " --> pdb=" O ARG R 258 " (cutoff:3.500A) Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 297 through 316 Processing helix chain 'R' and resid 317 through 326 Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 330 through 342 removed outlier: 3.940A pdb=" N ARG R 334 " --> pdb=" O GLY R 330 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 197 through 200 removed outlier: 3.746A pdb=" N ARG R 209 " --> pdb=" O GLN R 200 " (cutoff:3.500A) 194 hydrogen bonds defined for protein. 582 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: 0.57 Time building geometry restraints manager: 0.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 532 1.33 - 1.45: 630 1.45 - 1.57: 1611 1.57 - 1.69: 0 1.69 - 1.81: 26 Bond restraints: 2799 Sorted by residual: bond pdb=" N HIS R 165 " pdb=" CA HIS R 165 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.25e-02 6.40e+03 1.12e+01 bond pdb=" N GLN R 286 " pdb=" CA GLN R 286 " ideal model delta sigma weight residual 1.459 1.492 -0.032 1.19e-02 7.06e+03 7.37e+00 bond pdb=" C ASN R 305 " pdb=" O ASN R 305 " ideal model delta sigma weight residual 1.236 1.210 0.027 1.16e-02 7.43e+03 5.22e+00 bond pdb=" N ARG R 209 " pdb=" CA ARG R 209 " ideal model delta sigma weight residual 1.454 1.482 -0.027 1.27e-02 6.20e+03 4.55e+00 bond pdb=" N ARG R 54 " pdb=" CA ARG R 54 " ideal model delta sigma weight residual 1.459 1.484 -0.024 1.19e-02 7.06e+03 4.15e+00 ... (remaining 2794 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 3747 2.03 - 4.05: 56 4.05 - 6.08: 18 6.08 - 8.10: 3 8.10 - 10.13: 1 Bond angle restraints: 3825 Sorted by residual: angle pdb=" C PHE R 333 " pdb=" CA PHE R 333 " pdb=" CB PHE R 333 " ideal model delta sigma weight residual 110.85 120.98 -10.13 1.70e+00 3.46e-01 3.55e+01 angle pdb=" CA PHE R 333 " pdb=" CB PHE R 333 " pdb=" CG PHE R 333 " ideal model delta sigma weight residual 113.80 107.88 5.92 1.00e+00 1.00e+00 3.50e+01 angle pdb=" N ASN R 305 " pdb=" CA ASN R 305 " pdb=" C ASN R 305 " ideal model delta sigma weight residual 111.03 105.89 5.14 1.11e+00 8.12e-01 2.14e+01 angle pdb=" C GLY C 1 " pdb=" N THR C 2 " pdb=" CA THR C 2 " ideal model delta sigma weight residual 122.19 116.00 6.19 1.41e+00 5.03e-01 1.92e+01 angle pdb=" CA THR C 2 " pdb=" CB THR C 2 " pdb=" OG1 THR C 2 " ideal model delta sigma weight residual 109.60 103.07 6.53 1.50e+00 4.44e-01 1.89e+01 ... (remaining 3820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.39: 1475 11.39 - 22.78: 107 22.78 - 34.18: 42 34.18 - 45.57: 22 45.57 - 56.96: 12 Dihedral angle restraints: 1658 sinusoidal: 568 harmonic: 1090 Sorted by residual: dihedral pdb=" C PHE R 333 " pdb=" N PHE R 333 " pdb=" CA PHE R 333 " pdb=" CB PHE R 333 " ideal model delta harmonic sigma weight residual -122.60 -130.67 8.07 0 2.50e+00 1.60e-01 1.04e+01 dihedral pdb=" CA ARG R 166 " pdb=" CB ARG R 166 " pdb=" CG ARG R 166 " pdb=" CD ARG R 166 " ideal model delta sinusoidal sigma weight residual 180.00 123.04 56.96 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" N LYS R 130 " pdb=" CA LYS R 130 " pdb=" CB LYS R 130 " pdb=" CG LYS R 130 " ideal model delta sinusoidal sigma weight residual -60.00 -115.11 55.11 3 1.50e+01 4.44e-03 9.33e+00 ... (remaining 1655 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 338 0.038 - 0.075: 113 0.075 - 0.113: 25 0.113 - 0.151: 5 0.151 - 0.188: 2 Chirality restraints: 483 Sorted by residual: chirality pdb=" CA ARG R 166 " pdb=" N ARG R 166 " pdb=" C ARG R 166 " pdb=" CB ARG R 166 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.85e-01 chirality pdb=" CA HIS R 167 " pdb=" N HIS R 167 " pdb=" C HIS R 167 " pdb=" CB HIS R 167 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.42e-01 chirality pdb=" CB VAL C 36 " pdb=" CA VAL C 36 " pdb=" CG1 VAL C 36 " pdb=" CG2 VAL C 36 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.56e-01 ... (remaining 480 not shown) Planarity restraints: 465 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 166 " -0.426 9.50e-02 1.11e+02 1.91e-01 2.24e+01 pdb=" NE ARG R 166 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG R 166 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG R 166 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG R 166 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 164 " -0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C ALA R 164 " 0.061 2.00e-02 2.50e+03 pdb=" O ALA R 164 " -0.023 2.00e-02 2.50e+03 pdb=" N HIS R 165 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 209 " 0.309 9.50e-02 1.11e+02 1.38e-01 1.18e+01 pdb=" NE ARG R 209 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG R 209 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG R 209 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG R 209 " 0.010 2.00e-02 2.50e+03 ... (remaining 462 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.03: 1718 3.03 - 3.50: 3088 3.50 - 3.97: 4176 3.97 - 4.43: 4961 4.43 - 4.90: 7753 Nonbonded interactions: 21696 Sorted by model distance: nonbonded pdb=" NH1 ARG R 209 " pdb=" OG SER R 211 " model vdw 2.564 3.120 nonbonded pdb=" O ALA R 164 " pdb=" CA HIS R 165 " model vdw 2.614 2.776 nonbonded pdb=" O LEU R 304 " pdb=" CA ASN R 305 " model vdw 2.616 2.776 nonbonded pdb=" OD2 ASP C 4 " pdb=" NH1 ARG R 209 " model vdw 2.617 3.120 nonbonded pdb=" N GLN R 200 " pdb=" O GLN R 200 " model vdw 2.643 2.496 ... (remaining 21691 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.580 Find NCS groups from input model: 0.020 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:1.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6076 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 0.042 2802 Z= 0.213 Angle : 0.686 10.127 3831 Z= 0.440 Chirality : 0.040 0.188 483 Planarity : 0.012 0.191 465 Dihedral : 12.112 56.960 939 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 6.74 % Allowed : 7.45 % Favored : 85.82 % Cbeta Deviations : 0.28 % 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: 0.41 (0.46), residues: 363 helix: 1.75 (0.33), residues: 256 sheet: None (None), residues: 0 loop : -3.66 (0.53), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 166 TYR 0.005 0.001 TYR R 136 PHE 0.025 0.001 PHE R 333 TRP 0.008 0.001 TRP C 57 HIS 0.002 0.001 HIS R 165 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 2799) covalent geometry : angle 0.68557 ( 3825) SS BOND : bond 0.00360 ( 3) SS BOND : angle 0.85745 ( 6) hydrogen bonds : bond 0.09662 ( 194) hydrogen bonds : angle 4.97410 ( 582) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.105 Fit side-chains REVERT: C 36 VAL cc_start: 0.7823 (p) cc_final: 0.7555 (t) REVERT: R 138 MET cc_start: 0.5186 (ttp) cc_final: 0.4945 (ttm) REVERT: R 209 ARG cc_start: 0.4369 (ppt170) cc_final: 0.3922 (mmt90) REVERT: R 260 LYS cc_start: 0.6720 (tttp) cc_final: 0.6360 (pttp) REVERT: R 332 LYS cc_start: 0.6168 (OUTLIER) cc_final: 0.5036 (pttm) outliers start: 19 outliers final: 6 residues processed: 88 average time/residue: 0.0827 time to fit residues: 8.3511 Evaluate side-chains 59 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 27 TYR Chi-restraints excluded: chain R residue 129 CYS Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 210 CYS Chi-restraints excluded: chain R residue 332 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 13 optimal weight: 0.4980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 286 GLN R 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.212309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.185862 restraints weight = 3408.577| |-----------------------------------------------------------------------------| r_work (start): 0.4178 rms_B_bonded: 2.38 r_work: 0.4051 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3932 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2802 Z= 0.164 Angle : 0.652 6.716 3831 Z= 0.335 Chirality : 0.043 0.154 483 Planarity : 0.004 0.028 465 Dihedral : 6.742 51.273 403 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 4.96 % Allowed : 14.89 % Favored : 80.14 % 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: 0.12 (0.44), residues: 363 helix: 1.50 (0.32), residues: 257 sheet: None (None), residues: 0 loop : -3.75 (0.50), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 209 TYR 0.007 0.001 TYR R 96 PHE 0.009 0.002 PHE R 333 TRP 0.013 0.002 TRP C 57 HIS 0.002 0.001 HIS R 127 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 2799) covalent geometry : angle 0.64757 ( 3825) SS BOND : bond 0.00396 ( 3) SS BOND : angle 2.12415 ( 6) hydrogen bonds : bond 0.04368 ( 194) hydrogen bonds : angle 4.19724 ( 582) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.132 Fit side-chains REVERT: R 332 LYS cc_start: 0.5798 (OUTLIER) cc_final: 0.4699 (pttm) outliers start: 14 outliers final: 7 residues processed: 57 average time/residue: 0.0818 time to fit residues: 5.4833 Evaluate side-chains 53 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 27 TYR Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 156 VAL Chi-restraints excluded: chain R residue 332 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 31 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 7 optimal weight: 0.3980 chunk 27 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4425 r_free = 0.4425 target = 0.213864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.187166 restraints weight = 3437.153| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 2.36 r_work: 0.4014 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3909 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2802 Z= 0.141 Angle : 0.597 5.298 3831 Z= 0.308 Chirality : 0.042 0.151 483 Planarity : 0.003 0.030 465 Dihedral : 6.719 48.389 401 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 6.38 % Allowed : 14.54 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.45), residues: 363 helix: 1.63 (0.32), residues: 259 sheet: None (None), residues: 0 loop : -3.74 (0.49), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 209 TYR 0.006 0.001 TYR R 116 PHE 0.007 0.001 PHE C 41 TRP 0.011 0.002 TRP R 122 HIS 0.001 0.000 HIS R 127 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 2799) covalent geometry : angle 0.59429 ( 3825) SS BOND : bond 0.00239 ( 3) SS BOND : angle 1.65222 ( 6) hydrogen bonds : bond 0.04133 ( 194) hydrogen bonds : angle 4.04577 ( 582) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 51 time to evaluate : 0.103 Fit side-chains REVERT: R 332 LYS cc_start: 0.5869 (OUTLIER) cc_final: 0.4771 (pttm) outliers start: 18 outliers final: 11 residues processed: 60 average time/residue: 0.0580 time to fit residues: 4.3180 Evaluate side-chains 59 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 27 TYR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 228 MET Chi-restraints excluded: chain R residue 276 GLN Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 332 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 14 optimal weight: 0.2980 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.207162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.179409 restraints weight = 3397.001| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 2.26 r_work: 0.3959 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3845 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2802 Z= 0.150 Angle : 0.600 5.321 3831 Z= 0.310 Chirality : 0.041 0.152 483 Planarity : 0.004 0.030 465 Dihedral : 6.810 48.778 401 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 6.03 % Allowed : 18.09 % Favored : 75.89 % 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: 0.14 (0.44), residues: 363 helix: 1.53 (0.32), residues: 257 sheet: None (None), residues: 0 loop : -3.78 (0.48), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 54 TYR 0.006 0.001 TYR R 136 PHE 0.017 0.001 PHE R 241 TRP 0.013 0.002 TRP R 122 HIS 0.002 0.000 HIS R 127 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 2799) covalent geometry : angle 0.59744 ( 3825) SS BOND : bond 0.00318 ( 3) SS BOND : angle 1.49706 ( 6) hydrogen bonds : bond 0.04183 ( 194) hydrogen bonds : angle 4.08899 ( 582) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.112 Fit side-chains REVERT: C 48 GLN cc_start: 0.6384 (mt0) cc_final: 0.6031 (mt0) REVERT: R 73 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.6975 (tp) REVERT: R 241 PHE cc_start: 0.7596 (t80) cc_final: 0.7374 (t80) REVERT: R 332 LYS cc_start: 0.5906 (OUTLIER) cc_final: 0.4986 (pttm) REVERT: R 333 PHE cc_start: 0.7856 (m-80) cc_final: 0.7641 (m-80) outliers start: 17 outliers final: 9 residues processed: 62 average time/residue: 0.0570 time to fit residues: 4.3963 Evaluate side-chains 60 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 27 TYR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 228 MET Chi-restraints excluded: chain R residue 276 GLN Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 332 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 2 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 21 optimal weight: 0.0570 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.209223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.182705 restraints weight = 3358.333| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 2.15 r_work: 0.3958 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3843 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2802 Z= 0.142 Angle : 0.606 6.889 3831 Z= 0.311 Chirality : 0.041 0.148 483 Planarity : 0.003 0.031 465 Dihedral : 6.853 48.915 401 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 5.32 % Allowed : 19.15 % Favored : 75.53 % 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: 0.25 (0.45), residues: 363 helix: 1.60 (0.32), residues: 258 sheet: None (None), residues: 0 loop : -3.76 (0.48), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 258 TYR 0.006 0.001 TYR R 116 PHE 0.016 0.001 PHE R 241 TRP 0.013 0.002 TRP R 122 HIS 0.002 0.000 HIS R 127 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 2799) covalent geometry : angle 0.60384 ( 3825) SS BOND : bond 0.00340 ( 3) SS BOND : angle 1.44040 ( 6) hydrogen bonds : bond 0.04152 ( 194) hydrogen bonds : angle 4.07373 ( 582) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.106 Fit side-chains REVERT: C 36 VAL cc_start: 0.7717 (p) cc_final: 0.7451 (t) REVERT: R 73 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.6975 (tp) REVERT: R 208 MET cc_start: 0.5538 (mmm) cc_final: 0.5290 (mmm) REVERT: R 332 LYS cc_start: 0.5951 (OUTLIER) cc_final: 0.5108 (pttm) outliers start: 15 outliers final: 10 residues processed: 62 average time/residue: 0.0548 time to fit residues: 4.2284 Evaluate side-chains 61 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 27 TYR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 228 MET Chi-restraints excluded: chain R residue 276 GLN Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 332 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 22 optimal weight: 0.1980 chunk 5 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 0.2980 chunk 0 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 305 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.212426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.185193 restraints weight = 3373.566| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 2.19 r_work: 0.3970 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3854 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2802 Z= 0.132 Angle : 0.604 7.478 3831 Z= 0.307 Chirality : 0.040 0.150 483 Planarity : 0.003 0.031 465 Dihedral : 6.870 48.955 401 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 4.26 % Allowed : 21.99 % Favored : 73.76 % 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: 0.46 (0.45), residues: 363 helix: 1.76 (0.32), residues: 258 sheet: None (None), residues: 0 loop : -3.68 (0.49), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 258 TYR 0.005 0.001 TYR R 85 PHE 0.014 0.001 PHE R 86 TRP 0.013 0.002 TRP R 114 HIS 0.002 0.000 HIS R 127 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 2799) covalent geometry : angle 0.60178 ( 3825) SS BOND : bond 0.00298 ( 3) SS BOND : angle 1.40193 ( 6) hydrogen bonds : bond 0.04051 ( 194) hydrogen bonds : angle 4.05302 ( 582) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.060 Fit side-chains REVERT: C 36 VAL cc_start: 0.7721 (p) cc_final: 0.7466 (t) REVERT: C 48 GLN cc_start: 0.6355 (mt0) cc_final: 0.6039 (mt0) REVERT: R 73 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.6956 (tp) REVERT: R 208 MET cc_start: 0.5697 (mmm) cc_final: 0.5477 (mmm) REVERT: R 332 LYS cc_start: 0.5909 (OUTLIER) cc_final: 0.5157 (pttm) outliers start: 12 outliers final: 9 residues processed: 57 average time/residue: 0.0317 time to fit residues: 2.3247 Evaluate side-chains 58 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 27 TYR Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 228 MET Chi-restraints excluded: chain R residue 276 GLN Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 332 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 20 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.4372 r_free = 0.4372 target = 0.208851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.180211 restraints weight = 3324.578| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 2.34 r_work: 0.3960 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3840 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2802 Z= 0.183 Angle : 0.668 8.720 3831 Z= 0.341 Chirality : 0.043 0.155 483 Planarity : 0.004 0.032 465 Dihedral : 7.021 49.081 401 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 5.32 % Allowed : 21.28 % Favored : 73.40 % 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: -0.26 (0.44), residues: 363 helix: 1.19 (0.32), residues: 257 sheet: None (None), residues: 0 loop : -3.80 (0.48), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 258 TYR 0.010 0.002 TYR R 85 PHE 0.020 0.002 PHE R 241 TRP 0.018 0.003 TRP R 122 HIS 0.003 0.001 HIS R 127 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 2799) covalent geometry : angle 0.66523 ( 3825) SS BOND : bond 0.00390 ( 3) SS BOND : angle 1.62012 ( 6) hydrogen bonds : bond 0.04547 ( 194) hydrogen bonds : angle 4.32640 ( 582) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.063 Fit side-chains REVERT: C 36 VAL cc_start: 0.7792 (p) cc_final: 0.7565 (t) REVERT: C 48 GLN cc_start: 0.6413 (mt0) cc_final: 0.6048 (mt0) REVERT: R 73 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.6976 (tp) REVERT: R 208 MET cc_start: 0.5815 (mmm) cc_final: 0.5585 (mmm) REVERT: R 332 LYS cc_start: 0.6199 (OUTLIER) cc_final: 0.5422 (pttm) outliers start: 15 outliers final: 10 residues processed: 55 average time/residue: 0.0331 time to fit residues: 2.3062 Evaluate side-chains 57 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 27 TYR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 228 MET Chi-restraints excluded: chain R residue 276 GLN Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 332 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 5 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.211503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.184063 restraints weight = 3389.516| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 2.25 r_work: 0.3975 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3862 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 2802 Z= 0.159 Angle : 0.659 9.528 3831 Z= 0.332 Chirality : 0.042 0.158 483 Planarity : 0.004 0.033 465 Dihedral : 7.087 49.430 401 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 4.26 % Allowed : 22.70 % Favored : 73.05 % 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: -0.24 (0.44), residues: 363 helix: 1.21 (0.32), residues: 257 sheet: None (None), residues: 0 loop : -3.83 (0.48), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 258 TYR 0.013 0.002 TYR R 308 PHE 0.013 0.001 PHE R 86 TRP 0.014 0.002 TRP R 122 HIS 0.002 0.001 HIS R 127 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 2799) covalent geometry : angle 0.65701 ( 3825) SS BOND : bond 0.00352 ( 3) SS BOND : angle 1.47130 ( 6) hydrogen bonds : bond 0.04331 ( 194) hydrogen bonds : angle 4.21915 ( 582) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.109 Fit side-chains REVERT: C 36 VAL cc_start: 0.7743 (p) cc_final: 0.7529 (t) REVERT: C 48 GLN cc_start: 0.6268 (mt0) cc_final: 0.5898 (mt0) REVERT: R 73 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.6941 (tp) REVERT: R 332 LYS cc_start: 0.6178 (OUTLIER) cc_final: 0.5373 (pttm) outliers start: 12 outliers final: 9 residues processed: 56 average time/residue: 0.0517 time to fit residues: 3.5850 Evaluate side-chains 58 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 27 TYR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 228 MET Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 332 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 20 optimal weight: 0.8980 chunk 5 optimal weight: 0.2980 chunk 6 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 27 optimal weight: 0.3980 chunk 15 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4411 r_free = 0.4411 target = 0.213082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.185755 restraints weight = 3398.032| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 2.13 r_work: 0.3947 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3835 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2802 Z= 0.139 Angle : 0.637 10.426 3831 Z= 0.319 Chirality : 0.041 0.148 483 Planarity : 0.003 0.032 465 Dihedral : 7.088 50.398 401 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 4.26 % Allowed : 23.40 % Favored : 72.34 % 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: 0.04 (0.45), residues: 363 helix: 1.41 (0.32), residues: 258 sheet: None (None), residues: 0 loop : -3.70 (0.49), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 209 TYR 0.012 0.001 TYR R 279 PHE 0.010 0.001 PHE R 275 TRP 0.017 0.002 TRP R 114 HIS 0.002 0.000 HIS R 127 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 2799) covalent geometry : angle 0.63481 ( 3825) SS BOND : bond 0.00240 ( 3) SS BOND : angle 1.43113 ( 6) hydrogen bonds : bond 0.04133 ( 194) hydrogen bonds : angle 4.12392 ( 582) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.062 Fit side-chains REVERT: C 36 VAL cc_start: 0.7743 (p) cc_final: 0.7518 (t) REVERT: C 48 GLN cc_start: 0.6188 (mt0) cc_final: 0.5825 (mt0) REVERT: R 73 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.6964 (tp) REVERT: R 332 LYS cc_start: 0.5969 (OUTLIER) cc_final: 0.5341 (ptpt) outliers start: 12 outliers final: 9 residues processed: 53 average time/residue: 0.0347 time to fit residues: 2.3217 Evaluate side-chains 55 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 27 TYR Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 228 MET Chi-restraints excluded: chain R residue 276 GLN Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 332 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 13 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 27 optimal weight: 0.0570 chunk 20 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- 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 = 0.4396 r_free = 0.4396 target = 0.211444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.184555 restraints weight = 3442.303| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 2.30 r_work: 0.3939 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3823 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2802 Z= 0.157 Angle : 0.664 8.993 3831 Z= 0.334 Chirality : 0.042 0.153 483 Planarity : 0.004 0.033 465 Dihedral : 7.169 53.134 401 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 4.26 % Allowed : 23.40 % Favored : 72.34 % 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: -0.07 (0.45), residues: 363 helix: 1.34 (0.32), residues: 257 sheet: None (None), residues: 0 loop : -3.76 (0.49), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 209 TYR 0.010 0.002 TYR R 85 PHE 0.022 0.002 PHE R 241 TRP 0.033 0.003 TRP R 122 HIS 0.002 0.000 HIS R 127 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 2799) covalent geometry : angle 0.66166 ( 3825) SS BOND : bond 0.00304 ( 3) SS BOND : angle 1.52044 ( 6) hydrogen bonds : bond 0.04293 ( 194) hydrogen bonds : angle 4.21364 ( 582) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.068 Fit side-chains REVERT: C 36 VAL cc_start: 0.7770 (p) cc_final: 0.7557 (t) REVERT: C 48 GLN cc_start: 0.6243 (mt0) cc_final: 0.5868 (mt0) REVERT: R 73 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.6978 (tp) REVERT: R 332 LYS cc_start: 0.5994 (OUTLIER) cc_final: 0.5430 (ptpt) outliers start: 12 outliers final: 10 residues processed: 47 average time/residue: 0.0599 time to fit residues: 3.4321 Evaluate side-chains 52 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 27 TYR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 228 MET Chi-restraints excluded: chain R residue 276 GLN Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 332 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 20 optimal weight: 0.0870 chunk 10 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.7160 ------------------------------------------------------------------------------- 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 = 0.4396 r_free = 0.4396 target = 0.211630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.184182 restraints weight = 3384.176| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 2.27 r_work: 0.3936 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6706 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 2802 Z= 0.155 Angle : 0.663 9.810 3831 Z= 0.331 Chirality : 0.043 0.195 483 Planarity : 0.004 0.033 465 Dihedral : 7.212 55.955 401 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 4.26 % Allowed : 23.76 % Favored : 71.99 % 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: -0.09 (0.45), residues: 363 helix: 1.33 (0.32), residues: 257 sheet: None (None), residues: 0 loop : -3.76 (0.49), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 258 TYR 0.009 0.002 TYR R 85 PHE 0.015 0.001 PHE R 86 TRP 0.029 0.003 TRP R 122 HIS 0.002 0.000 HIS R 127 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 2799) covalent geometry : angle 0.66168 ( 3825) SS BOND : bond 0.00393 ( 3) SS BOND : angle 1.33654 ( 6) hydrogen bonds : bond 0.04277 ( 194) hydrogen bonds : angle 4.18306 ( 582) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 907.37 seconds wall clock time: 16 minutes 11.50 seconds (971.50 seconds total)