Starting phenix.real_space_refine on Tue Mar 3 10:47:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ubc_64004/03_2026/9ubc_64004.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ubc_64004/03_2026/9ubc_64004.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ubc_64004/03_2026/9ubc_64004.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ubc_64004/03_2026/9ubc_64004.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ubc_64004/03_2026/9ubc_64004.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ubc_64004/03_2026/9ubc_64004.map" } resolution = 3.43 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= 0.203 sd= 1.085 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 3 5.16 5 C 1020 2.51 5 N 306 2.21 5 O 317 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1649 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1481 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 9, 'TRANS': 179} Chain: "C" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 117 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ALY:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'ACO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.37, per 1000 atoms: 0.22 Number of scatterers: 1649 At special positions: 0 Unit cell: (60.663, 53.184, 59.001, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 3 16.00 P 3 15.00 O 317 8.00 N 306 7.00 C 1020 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.20 Conformation dependent library (CDL) restraints added in 40.8 milliseconds 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 356 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 1 sheets defined 40.7% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.03 Creating SS restraints... Processing helix chain 'A' and resid 22 through 24 No H-bonds generated for 'chain 'A' and resid 22 through 24' Processing helix chain 'A' and resid 25 through 34 Processing helix chain 'A' and resid 35 through 43 Processing helix chain 'A' and resid 49 through 63 removed outlier: 4.066A pdb=" N GLY A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N HIS A 59 " --> pdb=" O GLU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 108 removed outlier: 4.262A pdb=" N ARG A 108 " --> pdb=" O ALA A 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 105 through 108' Processing helix chain 'A' and resid 111 through 127 Processing helix chain 'A' and resid 141 through 152 Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'A' and resid 186 through 193 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.513A pdb=" N LEU A 11 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU A 68 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA A 87 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N PHE A 70 " --> pdb=" O THR A 85 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N THR A 85 " --> pdb=" O PHE A 70 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL A 72 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 81 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLY A 97 " --> pdb=" O HIS A 134 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ALA A 136 " --> pdb=" O GLY A 97 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N PHE A 99 " --> pdb=" O ALA A 136 " (cutoff:3.500A) removed outlier: 10.305A pdb=" N LEU A 138 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 12.896A pdb=" N ILE A 101 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 11.057A pdb=" N ARG A 168 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N SER A 162 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL A 170 " --> pdb=" O ARG A 160 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ARG A 160 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLU A 172 " --> pdb=" O GLU A 158 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLU A 158 " --> pdb=" O GLU A 172 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU A 174 " --> pdb=" O ILE A 156 " (cutoff:3.500A) 71 hydrogen bonds defined for protein. 201 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: 0.12 Time building geometry restraints manager: 0.15 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: 467 1.33 - 1.45: 315 1.45 - 1.57: 891 1.57 - 1.69: 9 1.69 - 1.81: 5 Bond restraints: 1687 Sorted by residual: bond pdb=" C6A ACO A 200 " pdb=" N6A ACO A 200 " ideal model delta sigma weight residual 1.337 1.383 -0.046 1.00e-02 1.00e+04 2.13e+01 bond pdb=" O5A ACO A 200 " pdb=" P2A ACO A 200 " ideal model delta sigma weight residual 1.529 1.610 -0.081 2.20e-02 2.07e+03 1.34e+01 bond pdb=" O2A ACO A 200 " pdb=" P1A ACO A 200 " ideal model delta sigma weight residual 1.529 1.608 -0.079 2.20e-02 2.07e+03 1.30e+01 bond pdb=" C5A ACO A 200 " pdb=" N7A ACO A 200 " ideal model delta sigma weight residual 1.387 1.354 0.033 1.00e-02 1.00e+04 1.10e+01 bond pdb=" C ACO A 200 " pdb=" S1P ACO A 200 " ideal model delta sigma weight residual 1.767 1.712 0.055 1.90e-02 2.77e+03 8.47e+00 ... (remaining 1682 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.40: 2282 5.40 - 10.80: 9 10.80 - 16.20: 2 16.20 - 21.59: 0 21.59 - 26.99: 1 Bond angle restraints: 2294 Sorted by residual: angle pdb=" P1A ACO A 200 " pdb=" O3A ACO A 200 " pdb=" P2A ACO A 200 " ideal model delta sigma weight residual 136.83 109.84 26.99 1.00e+00 1.00e+00 7.29e+02 angle pdb=" C3B ACO A 200 " pdb=" O3B ACO A 200 " pdb=" P3B ACO A 200 " ideal model delta sigma weight residual 121.12 106.12 15.00 1.00e+00 1.00e+00 2.25e+02 angle pdb=" C5B ACO A 200 " pdb=" O5B ACO A 200 " pdb=" P1A ACO A 200 " ideal model delta sigma weight residual 121.27 106.42 14.85 1.00e+00 1.00e+00 2.21e+02 angle pdb=" C5A ACO A 200 " pdb=" C4A ACO A 200 " pdb=" N3A ACO A 200 " ideal model delta sigma weight residual 126.80 119.08 7.72 1.00e+00 1.00e+00 5.97e+01 angle pdb=" CH3 ACO A 200 " pdb=" C ACO A 200 " pdb=" S1P ACO A 200 " ideal model delta sigma weight residual 112.98 120.06 -7.08 1.00e+00 1.00e+00 5.01e+01 ... (remaining 2289 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.77: 915 15.77 - 31.54: 49 31.54 - 47.31: 25 47.31 - 63.08: 8 63.08 - 78.85: 3 Dihedral angle restraints: 1000 sinusoidal: 435 harmonic: 565 Sorted by residual: dihedral pdb=" CA ARG C 12 " pdb=" CB ARG C 12 " pdb=" CG ARG C 12 " pdb=" CD ARG C 12 " ideal model delta sinusoidal sigma weight residual 60.00 110.73 -50.73 3 1.50e+01 4.44e-03 8.93e+00 dihedral pdb=" N ARG A 150 " pdb=" CA ARG A 150 " pdb=" CB ARG A 150 " pdb=" CG ARG A 150 " ideal model delta sinusoidal sigma weight residual -180.00 -130.66 -49.34 3 1.50e+01 4.44e-03 8.76e+00 dihedral pdb=" N GLU A 115 " pdb=" CA GLU A 115 " pdb=" CB GLU A 115 " pdb=" CG GLU A 115 " ideal model delta sinusoidal sigma weight residual -60.00 -100.54 40.54 3 1.50e+01 4.44e-03 7.23e+00 ... (remaining 997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 168 0.035 - 0.070: 48 0.070 - 0.105: 15 0.105 - 0.140: 3 0.140 - 0.175: 3 Chirality restraints: 237 Sorted by residual: chirality pdb=" C1B ACO A 200 " pdb=" C2B ACO A 200 " pdb=" N9A ACO A 200 " pdb=" O4B ACO A 200 " both_signs ideal model delta sigma weight residual False 2.41 2.58 -0.18 2.00e-01 2.50e+01 7.70e-01 chirality pdb=" CAP ACO A 200 " pdb=" C9P ACO A 200 " pdb=" CBP ACO A 200 " pdb=" OAP ACO A 200 " both_signs ideal model delta sigma weight residual False -2.31 -2.48 0.17 2.00e-01 2.50e+01 7.11e-01 chirality pdb=" C4B ACO A 200 " pdb=" C3B ACO A 200 " pdb=" C5B ACO A 200 " pdb=" O4B ACO A 200 " both_signs ideal model delta sigma weight residual False -2.52 -2.67 0.15 2.00e-01 2.50e+01 5.48e-01 ... (remaining 234 not shown) Planarity restraints: 302 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 139 " -0.015 5.00e-02 4.00e+02 2.20e-02 7.73e-01 pdb=" N PRO A 140 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO A 140 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 140 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 182 " -0.014 5.00e-02 4.00e+02 2.18e-02 7.58e-01 pdb=" N PRO A 183 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO A 183 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 183 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 35 " 0.014 5.00e-02 4.00e+02 2.13e-02 7.28e-01 pdb=" N PRO A 36 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO A 36 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 36 " 0.012 5.00e-02 4.00e+02 ... (remaining 299 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 373 2.78 - 3.31: 1501 3.31 - 3.84: 2688 3.84 - 4.37: 3140 4.37 - 4.90: 5534 Nonbonded interactions: 13236 Sorted by model distance: nonbonded pdb=" O6A ACO A 200 " pdb=" OAP ACO A 200 " model vdw 2.255 3.040 nonbonded pdb=" O LYS C 4 " pdb=" N ALA C 13 " model vdw 2.352 3.120 nonbonded pdb=" OE1 GLN A 60 " pdb=" NH2 ARG A 69 " model vdw 2.419 3.120 nonbonded pdb=" N LYS C 4 " pdb=" O ALA C 13 " model vdw 2.428 3.120 nonbonded pdb=" OD1 ASP A 122 " pdb=" ND1 HIS A 126 " model vdw 2.489 3.120 ... (remaining 13231 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.020 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 2.600 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 3.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 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 : 0.006 0.129 1688 Z= 0.446 Angle : 1.031 26.992 2294 Z= 0.875 Chirality : 0.042 0.175 237 Planarity : 0.003 0.022 302 Dihedral : 13.648 78.847 644 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.25 % Allowed : 3.75 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.59), residues: 197 helix: 2.59 (0.60), residues: 68 sheet: 0.03 (0.71), residues: 48 loop : -0.39 (0.68), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 159 TYR 0.007 0.001 TYR A 57 PHE 0.006 0.001 PHE A 21 TRP 0.002 0.001 TRP A 165 HIS 0.002 0.000 HIS A 107 Details of bonding type rmsd covalent geometry : bond 0.00555 ( 1687) covalent geometry : angle 1.03125 ( 2294) hydrogen bonds : bond 0.16560 ( 71) hydrogen bonds : angle 6.46511 ( 201) Misc. bond : bond 0.12892 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.033 Fit side-chains revert: symmetry clash REVERT: A 48 ASP cc_start: 0.8471 (t0) cc_final: 0.8140 (t0) REVERT: A 49 SER cc_start: 0.9207 (p) cc_final: 0.8795 (p) REVERT: A 51 GLU cc_start: 0.8528 (mp0) cc_final: 0.8252 (mp0) REVERT: A 66 ASP cc_start: 0.8433 (p0) cc_final: 0.8044 (p0) REVERT: A 135 LEU cc_start: 0.9412 (pp) cc_final: 0.9140 (pp) REVERT: A 148 TYR cc_start: 0.8779 (m-10) cc_final: 0.8530 (m-10) outliers start: 2 outliers final: 0 residues processed: 63 average time/residue: 0.0468 time to fit residues: 3.2464 Evaluate side-chains 50 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 12 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.076690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.065393 restraints weight = 4482.489| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.86 r_work: 0.2721 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 1688 Z= 0.150 Angle : 0.565 5.812 2294 Z= 0.300 Chirality : 0.043 0.130 237 Planarity : 0.004 0.034 302 Dihedral : 14.992 75.732 288 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.25 % Allowed : 16.25 % Favored : 82.50 % 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: 0.92 (0.58), residues: 197 helix: 2.38 (0.59), residues: 70 sheet: 0.24 (0.71), residues: 48 loop : -0.78 (0.65), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 44 TYR 0.006 0.001 TYR A 57 PHE 0.007 0.001 PHE A 21 TRP 0.002 0.001 TRP A 165 HIS 0.001 0.000 HIS A 107 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 1687) covalent geometry : angle 0.56548 ( 2294) hydrogen bonds : bond 0.03556 ( 71) hydrogen bonds : angle 5.25041 ( 201) Misc. bond : bond 0.00100 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.034 Fit side-chains revert: symmetry clash REVERT: A 49 SER cc_start: 0.9209 (p) cc_final: 0.7913 (p) REVERT: A 51 GLU cc_start: 0.8589 (mp0) cc_final: 0.8373 (pm20) REVERT: A 66 ASP cc_start: 0.8594 (p0) cc_final: 0.8244 (p0) REVERT: A 78 GLN cc_start: 0.8499 (tm-30) cc_final: 0.8285 (tm-30) outliers start: 2 outliers final: 1 residues processed: 52 average time/residue: 0.0488 time to fit residues: 2.8062 Evaluate side-chains 48 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 8 optimal weight: 8.9990 chunk 13 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 1 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.075307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.064397 restraints weight = 4720.412| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.90 r_work: 0.2690 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 1688 Z= 0.155 Angle : 0.574 7.028 2294 Z= 0.298 Chirality : 0.042 0.110 237 Planarity : 0.004 0.034 302 Dihedral : 14.628 77.382 288 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.12 % Allowed : 15.00 % Favored : 81.88 % 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: 0.73 (0.57), residues: 197 helix: 2.32 (0.61), residues: 70 sheet: 0.40 (0.76), residues: 43 loop : -1.09 (0.59), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 69 TYR 0.006 0.001 TYR A 57 PHE 0.018 0.001 PHE A 21 TRP 0.003 0.001 TRP A 165 HIS 0.001 0.000 HIS A 107 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 1687) covalent geometry : angle 0.57438 ( 2294) hydrogen bonds : bond 0.03315 ( 71) hydrogen bonds : angle 4.95928 ( 201) Misc. bond : bond 0.00084 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 SER cc_start: 0.9123 (p) cc_final: 0.7963 (p) REVERT: A 51 GLU cc_start: 0.8588 (mp0) cc_final: 0.8313 (pm20) REVERT: A 66 ASP cc_start: 0.8572 (p0) cc_final: 0.8196 (p0) outliers start: 5 outliers final: 3 residues processed: 52 average time/residue: 0.0450 time to fit residues: 2.6331 Evaluate side-chains 49 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 191 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 6 optimal weight: 10.0000 chunk 5 optimal weight: 0.4980 chunk 17 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 GLN ** C 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.076003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.064868 restraints weight = 4647.775| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 2.99 r_work: 0.2703 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 1688 Z= 0.139 Angle : 0.563 5.822 2294 Z= 0.289 Chirality : 0.042 0.114 237 Planarity : 0.004 0.029 302 Dihedral : 13.991 77.067 288 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.50 % Allowed : 17.50 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.57), residues: 197 helix: 2.45 (0.62), residues: 69 sheet: 0.53 (0.74), residues: 42 loop : -1.11 (0.59), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 44 TYR 0.009 0.001 TYR A 29 PHE 0.023 0.001 PHE A 21 TRP 0.002 0.000 TRP A 165 HIS 0.001 0.000 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 1687) covalent geometry : angle 0.56329 ( 2294) hydrogen bonds : bond 0.02967 ( 71) hydrogen bonds : angle 4.85136 ( 201) Misc. bond : bond 0.00093 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 SER cc_start: 0.9152 (p) cc_final: 0.7899 (p) REVERT: A 51 GLU cc_start: 0.8515 (mp0) cc_final: 0.8197 (pm20) REVERT: A 66 ASP cc_start: 0.8630 (p0) cc_final: 0.8283 (p0) outliers start: 4 outliers final: 4 residues processed: 44 average time/residue: 0.0433 time to fit residues: 2.1713 Evaluate side-chains 46 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 191 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 17 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 18 optimal weight: 20.0000 chunk 5 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 GLN ** C 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.074671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.063297 restraints weight = 4633.131| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 2.97 r_work: 0.2663 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 1688 Z= 0.201 Angle : 0.594 5.386 2294 Z= 0.316 Chirality : 0.044 0.123 237 Planarity : 0.004 0.028 302 Dihedral : 13.641 76.109 288 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.88 % Allowed : 18.12 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.57), residues: 197 helix: 2.26 (0.61), residues: 69 sheet: 0.32 (0.67), residues: 46 loop : -0.93 (0.62), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 168 TYR 0.012 0.002 TYR A 29 PHE 0.027 0.002 PHE A 21 TRP 0.006 0.001 TRP A 165 HIS 0.001 0.001 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 1687) covalent geometry : angle 0.59445 ( 2294) hydrogen bonds : bond 0.03300 ( 71) hydrogen bonds : angle 4.89684 ( 201) Misc. bond : bond 0.00054 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.059 Fit side-chains REVERT: A 49 SER cc_start: 0.9153 (p) cc_final: 0.7849 (p) REVERT: A 51 GLU cc_start: 0.8550 (mp0) cc_final: 0.8186 (pm20) REVERT: A 66 ASP cc_start: 0.8602 (p0) cc_final: 0.8251 (p0) outliers start: 3 outliers final: 3 residues processed: 43 average time/residue: 0.0867 time to fit residues: 4.1021 Evaluate side-chains 44 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 158 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 9 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN A 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.076167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.064967 restraints weight = 4562.900| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 2.92 r_work: 0.2694 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 1688 Z= 0.140 Angle : 0.592 6.471 2294 Z= 0.312 Chirality : 0.042 0.113 237 Planarity : 0.004 0.029 302 Dihedral : 13.391 75.599 288 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.50 % Allowed : 18.12 % Favored : 79.38 % 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: 0.63 (0.58), residues: 197 helix: 2.35 (0.61), residues: 69 sheet: 0.36 (0.75), residues: 42 loop : -1.21 (0.59), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 168 TYR 0.011 0.002 TYR A 29 PHE 0.020 0.001 PHE A 21 TRP 0.004 0.000 TRP A 165 HIS 0.001 0.000 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 1687) covalent geometry : angle 0.59183 ( 2294) hydrogen bonds : bond 0.02850 ( 71) hydrogen bonds : angle 4.75283 ( 201) Misc. bond : bond 0.00101 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.059 Fit side-chains REVERT: A 49 SER cc_start: 0.9066 (p) cc_final: 0.7854 (p) REVERT: A 51 GLU cc_start: 0.8520 (mp0) cc_final: 0.8196 (pm20) REVERT: A 66 ASP cc_start: 0.8590 (p0) cc_final: 0.8254 (p0) outliers start: 4 outliers final: 2 residues processed: 41 average time/residue: 0.0778 time to fit residues: 3.5605 Evaluate side-chains 40 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 78 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 16 optimal weight: 0.3980 chunk 7 optimal weight: 4.9990 chunk 18 optimal weight: 20.0000 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 GLN ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.076980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.065897 restraints weight = 4571.347| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.86 r_work: 0.2719 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 1688 Z= 0.127 Angle : 0.592 6.427 2294 Z= 0.313 Chirality : 0.041 0.113 237 Planarity : 0.004 0.025 302 Dihedral : 13.174 75.391 288 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.88 % Allowed : 19.38 % Favored : 78.75 % 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: 0.64 (0.58), residues: 197 helix: 2.33 (0.61), residues: 69 sheet: 0.45 (0.78), residues: 42 loop : -1.24 (0.60), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 168 TYR 0.011 0.001 TYR A 29 PHE 0.017 0.001 PHE A 21 TRP 0.003 0.000 TRP A 165 HIS 0.001 0.000 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 1687) covalent geometry : angle 0.59250 ( 2294) hydrogen bonds : bond 0.02735 ( 71) hydrogen bonds : angle 4.66966 ( 201) Misc. bond : bond 0.00107 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.060 Fit side-chains revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8580 (p0) cc_final: 0.8251 (p0) outliers start: 3 outliers final: 3 residues processed: 39 average time/residue: 0.0867 time to fit residues: 3.7682 Evaluate side-chains 42 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 191 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 12 optimal weight: 9.9990 chunk 15 optimal weight: 0.0980 chunk 1 optimal weight: 0.4980 chunk 4 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.076901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.065726 restraints weight = 4547.221| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.93 r_work: 0.2713 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1688 Z= 0.133 Angle : 0.627 6.278 2294 Z= 0.329 Chirality : 0.041 0.112 237 Planarity : 0.004 0.024 302 Dihedral : 13.038 75.345 288 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.25 % Allowed : 19.38 % Favored : 79.38 % 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: 0.73 (0.59), residues: 197 helix: 2.40 (0.62), residues: 69 sheet: 0.53 (0.79), residues: 42 loop : -1.19 (0.60), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 168 TYR 0.013 0.002 TYR A 29 PHE 0.015 0.001 PHE A 21 TRP 0.003 0.000 TRP A 165 HIS 0.001 0.000 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 1687) covalent geometry : angle 0.62662 ( 2294) hydrogen bonds : bond 0.02659 ( 71) hydrogen bonds : angle 4.62578 ( 201) Misc. bond : bond 0.00104 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.065 Fit side-chains revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8696 (mtm-85) cc_final: 0.8486 (mtm-85) REVERT: A 66 ASP cc_start: 0.8571 (p0) cc_final: 0.8251 (p0) outliers start: 2 outliers final: 2 residues processed: 40 average time/residue: 0.1034 time to fit residues: 4.5078 Evaluate side-chains 41 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 191 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 9 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.078019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.066857 restraints weight = 4566.390| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.91 r_work: 0.2730 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 1688 Z= 0.126 Angle : 0.617 7.326 2294 Z= 0.325 Chirality : 0.041 0.111 237 Planarity : 0.004 0.024 302 Dihedral : 12.842 75.305 288 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.88 % Allowed : 19.38 % Favored : 78.75 % 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: 0.67 (0.58), residues: 197 helix: 2.40 (0.61), residues: 69 sheet: 0.60 (0.81), residues: 42 loop : -1.35 (0.58), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 168 TYR 0.014 0.002 TYR A 29 PHE 0.014 0.001 PHE A 21 TRP 0.002 0.000 TRP A 30 HIS 0.001 0.000 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 1687) covalent geometry : angle 0.61675 ( 2294) hydrogen bonds : bond 0.02627 ( 71) hydrogen bonds : angle 4.56832 ( 201) Misc. bond : bond 0.00107 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.063 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.7693 (pm20) cc_final: 0.7322 (pm20) REVERT: A 66 ASP cc_start: 0.8541 (p0) cc_final: 0.8235 (p0) outliers start: 3 outliers final: 2 residues processed: 42 average time/residue: 0.1001 time to fit residues: 4.5839 Evaluate side-chains 43 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 191 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 12 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 chunk 1 optimal weight: 0.3980 chunk 11 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 overall best weight: 2.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.075392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.064350 restraints weight = 4537.802| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.87 r_work: 0.2677 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 1688 Z= 0.176 Angle : 0.676 7.374 2294 Z= 0.354 Chirality : 0.042 0.111 237 Planarity : 0.004 0.025 302 Dihedral : 12.602 68.591 288 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.62 % Allowed : 20.00 % Favored : 79.38 % 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: 0.58 (0.57), residues: 197 helix: 2.23 (0.61), residues: 69 sheet: 0.35 (0.72), residues: 47 loop : -1.27 (0.60), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 44 TYR 0.010 0.002 TYR A 29 PHE 0.021 0.001 PHE A 21 TRP 0.003 0.001 TRP A 165 HIS 0.001 0.000 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 1687) covalent geometry : angle 0.67583 ( 2294) hydrogen bonds : bond 0.03135 ( 71) hydrogen bonds : angle 4.70545 ( 201) Misc. bond : bond 0.00056 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.065 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.7787 (pm20) cc_final: 0.7388 (pm20) REVERT: A 66 ASP cc_start: 0.8594 (p0) cc_final: 0.8262 (p0) outliers start: 1 outliers final: 1 residues processed: 40 average time/residue: 0.0968 time to fit residues: 4.2274 Evaluate side-chains 41 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 6 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 18 optimal weight: 20.0000 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.076342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.065339 restraints weight = 4565.116| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.81 r_work: 0.2692 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 1688 Z= 0.149 Angle : 0.648 7.258 2294 Z= 0.339 Chirality : 0.041 0.111 237 Planarity : 0.004 0.025 302 Dihedral : 12.511 70.340 288 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.62 % Allowed : 19.38 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.58), residues: 197 helix: 2.29 (0.61), residues: 69 sheet: 0.30 (0.73), residues: 47 loop : -1.30 (0.60), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 44 TYR 0.017 0.002 TYR A 29 PHE 0.017 0.001 PHE A 21 TRP 0.003 0.000 TRP A 165 HIS 0.001 0.000 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 1687) covalent geometry : angle 0.64796 ( 2294) hydrogen bonds : bond 0.02905 ( 71) hydrogen bonds : angle 4.64991 ( 201) Misc. bond : bond 0.00082 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 534.19 seconds wall clock time: 9 minutes 55.94 seconds (595.94 seconds total)