Starting phenix.real_space_refine on Fri Aug 22 12:36:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3jbs_6478/08_2025/3jbs_6478.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jbs_6478/08_2025/3jbs_6478.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/3jbs_6478/08_2025/3jbs_6478.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jbs_6478/08_2025/3jbs_6478.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/3jbs_6478/08_2025/3jbs_6478.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jbs_6478/08_2025/3jbs_6478.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 1 5.16 5 C 902 2.51 5 N 251 2.21 5 O 247 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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1401 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1401 Classifications: {'peptide': 175} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 165} Time building chain proxies: 0.41, per 1000 atoms: 0.29 Number of scatterers: 1401 At special positions: 0 Unit cell: (103.49, 69.43, 60.26, 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 1 16.00 O 247 8.00 N 251 7.00 C 902 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.06 Conformation dependent library (CDL) restraints added in 40.4 milliseconds Enol-peptide restraints added in 1.2 microseconds 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 336 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 1 sheets defined 29.7% alpha, 12.0% 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 68 through 73 Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 112 through 122 Processing helix chain 'A' and resid 123 through 126 Processing helix chain 'A' and resid 131 through 150 Processing helix chain 'A' and resid 154 through 161 Processing sheet with id=A, first strand: chain 'A' and resid 77 through 79 removed outlier: 6.418A pdb=" N LEU A 64 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR A 38 " --> pdb=" O TYR A 54 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N THR A 89 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ILE A 41 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N THR A 87 " --> pdb=" O ILE A 41 " (cutoff:3.500A) 41 hydrogen bonds defined for protein. 114 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: 0.09 Time building geometry restraints manager: 0.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.32: 275 1.32 - 1.44: 282 1.44 - 1.56: 866 1.56 - 1.68: 0 1.68 - 1.80: 2 Bond restraints: 1425 Sorted by residual: bond pdb=" CG ASP A 142 " pdb=" OD2 ASP A 142 " ideal model delta sigma weight residual 1.249 1.205 0.044 1.90e-02 2.77e+03 5.32e+00 bond pdb=" CD GLU A 124 " pdb=" OE1 GLU A 124 " ideal model delta sigma weight residual 1.249 1.206 0.043 1.90e-02 2.77e+03 5.13e+00 bond pdb=" CG ASP A 60 " pdb=" OD2 ASP A 60 " ideal model delta sigma weight residual 1.249 1.206 0.043 1.90e-02 2.77e+03 5.07e+00 bond pdb=" CG ASP A 169 " pdb=" OD2 ASP A 169 " ideal model delta sigma weight residual 1.249 1.206 0.043 1.90e-02 2.77e+03 5.03e+00 bond pdb=" CG ASP A 14 " pdb=" OD2 ASP A 14 " ideal model delta sigma weight residual 1.249 1.206 0.043 1.90e-02 2.77e+03 5.02e+00 ... (remaining 1420 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 1740 1.97 - 3.93: 136 3.93 - 5.89: 26 5.89 - 7.86: 8 7.86 - 9.82: 4 Bond angle restraints: 1914 Sorted by residual: angle pdb=" C LYS A 170 " pdb=" N PRO A 171 " pdb=" CA PRO A 171 " ideal model delta sigma weight residual 119.47 129.29 -9.82 1.16e+00 7.43e-01 7.17e+01 angle pdb=" C VAL A 74 " pdb=" N PRO A 75 " pdb=" CA PRO A 75 " ideal model delta sigma weight residual 120.03 127.80 -7.77 9.90e-01 1.02e+00 6.17e+01 angle pdb=" C THR A 152 " pdb=" N PRO A 153 " pdb=" CA PRO A 153 " ideal model delta sigma weight residual 119.56 127.47 -7.91 1.02e+00 9.61e-01 6.01e+01 angle pdb=" C ARG A 26 " pdb=" N PRO A 27 " pdb=" CA PRO A 27 " ideal model delta sigma weight residual 119.78 127.47 -7.69 1.03e+00 9.43e-01 5.58e+01 angle pdb=" C PHE A 122 " pdb=" N PRO A 123 " pdb=" CA PRO A 123 " ideal model delta sigma weight residual 119.28 127.41 -8.13 1.10e+00 8.26e-01 5.47e+01 ... (remaining 1909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.52: 861 11.52 - 23.04: 25 23.04 - 34.57: 5 34.57 - 46.09: 1 46.09 - 57.61: 8 Dihedral angle restraints: 900 sinusoidal: 385 harmonic: 515 Sorted by residual: dihedral pdb=" CA TYR A 54 " pdb=" CB TYR A 54 " pdb=" CG TYR A 54 " pdb=" CD1 TYR A 54 " ideal model delta sinusoidal sigma weight residual 90.00 37.54 52.46 2 2.00e+01 2.50e-03 7.54e+00 dihedral pdb=" C ARG A 82 " pdb=" N ARG A 82 " pdb=" CA ARG A 82 " pdb=" CB ARG A 82 " ideal model delta harmonic sigma weight residual -122.60 -116.51 -6.09 0 2.50e+00 1.60e-01 5.93e+00 dihedral pdb=" CA GLU A 59 " pdb=" CB GLU A 59 " pdb=" CG GLU A 59 " pdb=" CD GLU A 59 " ideal model delta sinusoidal sigma weight residual 60.00 87.37 -27.37 3 1.50e+01 4.44e-03 4.09e+00 ... (remaining 897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 110 0.040 - 0.079: 66 0.079 - 0.119: 31 0.119 - 0.158: 5 0.158 - 0.198: 5 Chirality restraints: 217 Sorted by residual: chirality pdb=" CA VAL A 91 " pdb=" N VAL A 91 " pdb=" C VAL A 91 " pdb=" CB VAL A 91 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.77e-01 chirality pdb=" CA ALA A 81 " pdb=" N ALA A 81 " pdb=" C ALA A 81 " pdb=" CB ALA A 81 " both_signs ideal model delta sigma weight residual False 2.48 2.31 0.18 2.00e-01 2.50e+01 7.68e-01 chirality pdb=" CA VAL A 35 " pdb=" N VAL A 35 " pdb=" C VAL A 35 " pdb=" CB VAL A 35 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.37e-01 ... (remaining 214 not shown) Planarity restraints: 241 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 176 " -0.014 2.00e-02 2.50e+03 2.78e-02 7.72e+00 pdb=" C PHE A 176 " 0.048 2.00e-02 2.50e+03 pdb=" O PHE A 176 " -0.017 2.00e-02 2.50e+03 pdb=" OXT PHE A 176 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 54 " -0.024 2.00e-02 2.50e+03 1.35e-02 3.65e+00 pdb=" CG TYR A 54 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 TYR A 54 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR A 54 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A 54 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 54 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 54 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 54 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 152 " 0.032 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO A 153 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 153 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 153 " 0.024 5.00e-02 4.00e+02 ... (remaining 238 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 681 2.99 - 3.47: 1292 3.47 - 3.94: 2189 3.94 - 4.42: 2289 4.42 - 4.90: 3627 Nonbonded interactions: 10078 Sorted by model distance: nonbonded pdb=" O VAL A 35 " pdb=" OG1 THR A 38 " model vdw 2.510 3.040 nonbonded pdb=" O PHE A 122 " pdb=" CB PHE A 122 " model vdw 2.604 2.752 nonbonded pdb=" O GLY A 67 " pdb=" CD PRO A 68 " model vdw 2.616 2.752 nonbonded pdb=" OH TYR A 105 " pdb=" OD2 ASP A 137 " model vdw 2.628 3.040 nonbonded pdb=" N TYR A 83 " pdb=" N VAL A 84 " model vdw 2.631 2.560 ... (remaining 10073 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 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: 0.010 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 2.210 Find NCS groups from input model: 0.000 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:4.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 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 : 0.010 0.044 1425 Z= 0.594 Angle : 1.322 9.824 1914 Z= 0.943 Chirality : 0.061 0.198 217 Planarity : 0.007 0.048 241 Dihedral : 8.674 57.610 564 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 aren not related in a simple way. whole: 0.51 (0.60), residues: 173 helix: 0.62 (0.74), residues: 45 sheet: -2.37 (1.27), residues: 11 loop : 0.66 (0.55), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 134 TYR 0.024 0.005 TYR A 54 PHE 0.020 0.004 PHE A 101 TRP 0.011 0.005 TRP A 9 HIS 0.006 0.002 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.01008 ( 1425) covalent geometry : angle 1.32210 ( 1914) hydrogen bonds : bond 0.13940 ( 41) hydrogen bonds : angle 6.93602 ( 114) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.033 Fit side-chains REVERT: A 80 ASN cc_start: 0.8572 (t0) cc_final: 0.8356 (t0) REVERT: A 82 ARG cc_start: 0.7796 (mmt180) cc_final: 0.7045 (mtt180) REVERT: A 108 LYS cc_start: 0.3358 (mttt) cc_final: 0.2411 (tptp) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.6220 time to fit residues: 34.4877 Evaluate side-chains 20 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A 167 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.149543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.123934 restraints weight = 2701.041| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.43 r_work: 0.3560 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1425 Z= 0.131 Angle : 0.554 4.293 1914 Z= 0.297 Chirality : 0.043 0.128 217 Planarity : 0.005 0.035 241 Dihedral : 4.082 28.179 190 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.61 % Allowed : 15.13 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 aren not related in a simple way. whole: 1.50 (0.63), residues: 173 helix: 1.88 (0.75), residues: 45 sheet: -1.40 (1.36), residues: 10 loop : 1.04 (0.59), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 134 TYR 0.005 0.001 TYR A 158 PHE 0.005 0.001 PHE A 122 TRP 0.000 0.000 TRP A 9 HIS 0.001 0.001 HIS A 172 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 1425) covalent geometry : angle 0.55432 ( 1914) hydrogen bonds : bond 0.05036 ( 41) hydrogen bonds : angle 6.11563 ( 114) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.070 Fit side-chains REVERT: A 82 ARG cc_start: 0.8424 (mmt180) cc_final: 0.7082 (mtt180) REVERT: A 91 VAL cc_start: 0.7881 (t) cc_final: 0.7445 (m) REVERT: A 108 LYS cc_start: 0.2105 (mttt) cc_final: 0.0623 (tptp) REVERT: A 122 PHE cc_start: 0.5747 (OUTLIER) cc_final: 0.4730 (m-80) REVERT: A 136 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7340 (mm-30) outliers start: 7 outliers final: 1 residues processed: 31 average time/residue: 0.4191 time to fit residues: 13.2232 Evaluate side-chains 31 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 122 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 15 optimal weight: 7.9990 chunk 2 optimal weight: 0.0070 chunk 11 optimal weight: 20.0000 chunk 9 optimal weight: 40.0000 chunk 4 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.147541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.122622 restraints weight = 2661.077| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.34 r_work: 0.3549 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 1425 Z= 0.101 Angle : 0.477 5.571 1914 Z= 0.245 Chirality : 0.040 0.123 217 Planarity : 0.004 0.029 241 Dihedral : 3.870 28.753 190 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 4.61 % Allowed : 22.37 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 aren not related in a simple way. whole: 1.35 (0.65), residues: 173 helix: 1.97 (0.76), residues: 45 sheet: -2.04 (1.09), residues: 18 loop : 1.16 (0.63), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 134 TYR 0.005 0.001 TYR A 158 PHE 0.003 0.001 PHE A 106 TRP 0.001 0.000 TRP A 9 HIS 0.001 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 1425) covalent geometry : angle 0.47692 ( 1914) hydrogen bonds : bond 0.04493 ( 41) hydrogen bonds : angle 5.55224 ( 114) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.062 Fit side-chains REVERT: A 19 LYS cc_start: 0.8307 (mttt) cc_final: 0.7578 (mttp) REVERT: A 82 ARG cc_start: 0.8541 (mmt180) cc_final: 0.6972 (mtt180) REVERT: A 91 VAL cc_start: 0.8237 (t) cc_final: 0.7794 (m) REVERT: A 97 ASN cc_start: 0.7571 (t0) cc_final: 0.7336 (t0) REVERT: A 108 LYS cc_start: 0.2460 (mttt) cc_final: 0.1176 (tptm) REVERT: A 122 PHE cc_start: 0.5344 (OUTLIER) cc_final: 0.4716 (m-80) REVERT: A 136 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7421 (mm-30) outliers start: 7 outliers final: 4 residues processed: 32 average time/residue: 0.5277 time to fit residues: 17.1751 Evaluate side-chains 30 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 12 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 0.3980 chunk 4 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 167 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.143257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.117842 restraints weight = 2637.563| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.30 r_work: 0.3484 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.5372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1425 Z= 0.112 Angle : 0.497 5.533 1914 Z= 0.260 Chirality : 0.042 0.124 217 Planarity : 0.004 0.024 241 Dihedral : 3.847 27.759 190 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 5.26 % Allowed : 21.71 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 aren not related in a simple way. whole: 0.93 (0.65), residues: 173 helix: 1.29 (0.76), residues: 45 sheet: -1.99 (1.17), residues: 18 loop : 0.99 (0.62), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 51 TYR 0.005 0.001 TYR A 158 PHE 0.003 0.001 PHE A 47 TRP 0.001 0.000 TRP A 9 HIS 0.002 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 1425) covalent geometry : angle 0.49725 ( 1914) hydrogen bonds : bond 0.04614 ( 41) hydrogen bonds : angle 5.71355 ( 114) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.063 Fit side-chains REVERT: A 19 LYS cc_start: 0.8446 (mttt) cc_final: 0.7570 (mtmm) REVERT: A 82 ARG cc_start: 0.8722 (mmt180) cc_final: 0.7018 (mtt180) REVERT: A 91 VAL cc_start: 0.8187 (t) cc_final: 0.7684 (m) REVERT: A 108 LYS cc_start: 0.2993 (mttt) cc_final: 0.1166 (tptm) REVERT: A 122 PHE cc_start: 0.5427 (OUTLIER) cc_final: 0.4863 (m-80) REVERT: A 124 GLU cc_start: 0.4832 (mm-30) cc_final: 0.3890 (pt0) REVERT: A 136 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7402 (mm-30) outliers start: 8 outliers final: 2 residues processed: 29 average time/residue: 0.4786 time to fit residues: 14.1489 Evaluate side-chains 25 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 155 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 7 optimal weight: 3.9990 chunk 2 optimal weight: 0.0000 chunk 4 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 9 optimal weight: 0.0070 chunk 16 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.142646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.117864 restraints weight = 2622.711| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.27 r_work: 0.3479 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.5782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 1425 Z= 0.107 Angle : 0.477 5.070 1914 Z= 0.246 Chirality : 0.041 0.123 217 Planarity : 0.004 0.024 241 Dihedral : 3.838 26.471 190 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 5.92 % Allowed : 23.68 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 aren not related in a simple way. whole: 0.92 (0.65), residues: 173 helix: 1.40 (0.78), residues: 45 sheet: -2.02 (1.21), residues: 18 loop : 0.93 (0.61), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 134 TYR 0.005 0.001 TYR A 158 PHE 0.004 0.001 PHE A 47 TRP 0.001 0.000 TRP A 9 HIS 0.002 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 1425) covalent geometry : angle 0.47713 ( 1914) hydrogen bonds : bond 0.04422 ( 41) hydrogen bonds : angle 5.70907 ( 114) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 20 time to evaluate : 0.078 Fit side-chains REVERT: A 82 ARG cc_start: 0.8391 (mmt180) cc_final: 0.6801 (mtt180) REVERT: A 108 LYS cc_start: 0.2744 (mttt) cc_final: 0.1202 (tptm) REVERT: A 122 PHE cc_start: 0.5267 (OUTLIER) cc_final: 0.4682 (m-80) REVERT: A 124 GLU cc_start: 0.4757 (mm-30) cc_final: 0.3851 (pt0) REVERT: A 136 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7324 (mm-30) outliers start: 9 outliers final: 4 residues processed: 25 average time/residue: 0.5727 time to fit residues: 14.5653 Evaluate side-chains 23 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 10 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.136638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.112566 restraints weight = 2640.956| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.19 r_work: 0.3396 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.6471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 1425 Z= 0.200 Angle : 0.611 6.320 1914 Z= 0.316 Chirality : 0.044 0.125 217 Planarity : 0.005 0.032 241 Dihedral : 4.336 22.687 190 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 5.92 % Allowed : 25.00 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 aren not related in a simple way. whole: 0.49 (0.64), residues: 173 helix: 1.08 (0.80), residues: 39 sheet: -2.02 (1.26), residues: 18 loop : 0.61 (0.59), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 51 TYR 0.010 0.002 TYR A 105 PHE 0.007 0.001 PHE A 47 TRP 0.002 0.001 TRP A 9 HIS 0.003 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 1425) covalent geometry : angle 0.61063 ( 1914) hydrogen bonds : bond 0.06101 ( 41) hydrogen bonds : angle 6.29728 ( 114) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 20 time to evaluate : 0.063 Fit side-chains REVERT: A 5 LYS cc_start: 0.5213 (tppt) cc_final: 0.4520 (mttt) REVERT: A 60 ASP cc_start: 0.8323 (p0) cc_final: 0.7787 (p0) REVERT: A 82 ARG cc_start: 0.8713 (mmt180) cc_final: 0.6800 (mtt180) REVERT: A 108 LYS cc_start: 0.3483 (mttt) cc_final: 0.0776 (tptm) REVERT: A 122 PHE cc_start: 0.5469 (OUTLIER) cc_final: 0.4848 (m-80) REVERT: A 136 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7211 (mm-30) outliers start: 9 outliers final: 5 residues processed: 25 average time/residue: 0.5567 time to fit residues: 14.1657 Evaluate side-chains 25 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 5 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 4 optimal weight: 0.0670 chunk 13 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.140557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.116601 restraints weight = 2626.862| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.19 r_work: 0.3459 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.6547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 1425 Z= 0.106 Angle : 0.516 7.339 1914 Z= 0.265 Chirality : 0.042 0.140 217 Planarity : 0.004 0.022 241 Dihedral : 4.096 28.601 190 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 4.61 % Allowed : 26.97 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 aren not related in a simple way. whole: 0.84 (0.65), residues: 173 helix: 1.55 (0.80), residues: 39 sheet: -1.90 (1.20), residues: 18 loop : 0.78 (0.61), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 134 TYR 0.005 0.001 TYR A 158 PHE 0.004 0.001 PHE A 47 TRP 0.001 0.000 TRP A 9 HIS 0.003 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 1425) covalent geometry : angle 0.51582 ( 1914) hydrogen bonds : bond 0.04636 ( 41) hydrogen bonds : angle 5.83435 ( 114) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.044 Fit side-chains REVERT: A 5 LYS cc_start: 0.4775 (tppt) cc_final: 0.3953 (mttp) REVERT: A 19 LYS cc_start: 0.8418 (mttt) cc_final: 0.6782 (mptt) REVERT: A 60 ASP cc_start: 0.8120 (p0) cc_final: 0.7659 (p0) REVERT: A 82 ARG cc_start: 0.8682 (mmt180) cc_final: 0.6830 (mtt180) REVERT: A 108 LYS cc_start: 0.3346 (mttt) cc_final: 0.1352 (tptm) REVERT: A 122 PHE cc_start: 0.5366 (OUTLIER) cc_final: 0.4771 (m-80) REVERT: A 124 GLU cc_start: 0.4795 (mm-30) cc_final: 0.3719 (pt0) REVERT: A 136 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7271 (mm-30) outliers start: 7 outliers final: 3 residues processed: 24 average time/residue: 0.6625 time to fit residues: 16.1529 Evaluate side-chains 23 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 155 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 4 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.3819 r_free = 0.3819 target = 0.136387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.112580 restraints weight = 2601.886| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.19 r_work: 0.3397 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.6828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 1425 Z= 0.173 Angle : 0.573 7.537 1914 Z= 0.296 Chirality : 0.043 0.134 217 Planarity : 0.004 0.027 241 Dihedral : 4.269 23.657 190 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 4.61 % Allowed : 25.66 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 aren not related in a simple way. whole: 0.56 (0.64), residues: 173 helix: 1.40 (0.82), residues: 39 sheet: -2.00 (1.20), residues: 18 loop : 0.55 (0.59), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 51 TYR 0.009 0.001 TYR A 105 PHE 0.005 0.001 PHE A 47 TRP 0.002 0.001 TRP A 9 HIS 0.002 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 1425) covalent geometry : angle 0.57300 ( 1914) hydrogen bonds : bond 0.05685 ( 41) hydrogen bonds : angle 6.20671 ( 114) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 17 time to evaluate : 0.065 Fit side-chains REVERT: A 5 LYS cc_start: 0.5270 (tppt) cc_final: 0.3956 (mttp) REVERT: A 60 ASP cc_start: 0.8158 (p0) cc_final: 0.7735 (p0) REVERT: A 82 ARG cc_start: 0.8727 (mmt180) cc_final: 0.6840 (mtt180) REVERT: A 108 LYS cc_start: 0.3302 (mttt) cc_final: 0.1017 (tptm) REVERT: A 122 PHE cc_start: 0.5896 (OUTLIER) cc_final: 0.5205 (m-80) REVERT: A 124 GLU cc_start: 0.4827 (mm-30) cc_final: 0.3751 (pt0) REVERT: A 136 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7277 (mm-30) outliers start: 7 outliers final: 5 residues processed: 23 average time/residue: 0.5592 time to fit residues: 13.0738 Evaluate side-chains 23 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 17 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 9 optimal weight: 30.0000 chunk 16 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.3839 r_free = 0.3839 target = 0.137903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.114442 restraints weight = 2696.495| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.23 r_work: 0.3422 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.6915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 1425 Z= 0.133 Angle : 0.536 8.078 1914 Z= 0.279 Chirality : 0.042 0.130 217 Planarity : 0.004 0.023 241 Dihedral : 4.173 26.630 190 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.29 % Allowed : 28.95 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 aren not related in a simple way. whole: 0.62 (0.65), residues: 173 helix: 1.55 (0.84), residues: 39 sheet: -2.02 (1.18), residues: 18 loop : 0.56 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 51 TYR 0.007 0.001 TYR A 105 PHE 0.005 0.001 PHE A 47 TRP 0.001 0.000 TRP A 9 HIS 0.002 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 1425) covalent geometry : angle 0.53649 ( 1914) hydrogen bonds : bond 0.04956 ( 41) hydrogen bonds : angle 6.10073 ( 114) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 0.060 Fit side-chains REVERT: A 5 LYS cc_start: 0.5245 (tppt) cc_final: 0.3989 (mttp) REVERT: A 60 ASP cc_start: 0.8205 (p0) cc_final: 0.7916 (p0) REVERT: A 82 ARG cc_start: 0.8753 (mmt180) cc_final: 0.6895 (mtt180) REVERT: A 108 LYS cc_start: 0.3047 (mttt) cc_final: 0.0989 (tptm) REVERT: A 117 LYS cc_start: 0.6115 (mtmt) cc_final: 0.5821 (mttt) REVERT: A 122 PHE cc_start: 0.5755 (OUTLIER) cc_final: 0.5117 (m-80) REVERT: A 124 GLU cc_start: 0.4981 (mm-30) cc_final: 0.3750 (pt0) REVERT: A 136 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7285 (mm-30) outliers start: 5 outliers final: 4 residues processed: 21 average time/residue: 0.6064 time to fit residues: 12.9490 Evaluate side-chains 23 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 155 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 0 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 9 optimal weight: 20.0000 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 3 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.3834 r_free = 0.3834 target = 0.137461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.114018 restraints weight = 2645.281| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.20 r_work: 0.3417 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.7026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 1425 Z= 0.144 Angle : 0.558 8.810 1914 Z= 0.291 Chirality : 0.042 0.127 217 Planarity : 0.004 0.025 241 Dihedral : 4.188 25.148 190 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 3.29 % Allowed : 28.29 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 aren not related in a simple way. whole: 0.58 (0.65), residues: 173 helix: 1.47 (0.84), residues: 39 sheet: -2.01 (1.19), residues: 18 loop : 0.54 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 51 TYR 0.007 0.001 TYR A 105 PHE 0.005 0.001 PHE A 47 TRP 0.001 0.001 TRP A 9 HIS 0.002 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 1425) covalent geometry : angle 0.55756 ( 1914) hydrogen bonds : bond 0.05120 ( 41) hydrogen bonds : angle 6.20627 ( 114) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 346 Ramachandran restraints generated. 173 Oldfield, 0 Emsley, 173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 0.036 Fit side-chains REVERT: A 5 LYS cc_start: 0.5626 (tppt) cc_final: 0.4376 (mttp) REVERT: A 60 ASP cc_start: 0.8362 (p0) cc_final: 0.8098 (p0) REVERT: A 82 ARG cc_start: 0.8761 (mmt180) cc_final: 0.6891 (mtt180) REVERT: A 108 LYS cc_start: 0.3163 (mttt) cc_final: 0.0993 (tptm) REVERT: A 117 LYS cc_start: 0.6202 (mtmt) cc_final: 0.5939 (mttt) REVERT: A 122 PHE cc_start: 0.5856 (OUTLIER) cc_final: 0.5156 (m-80) REVERT: A 136 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7335 (mm-30) outliers start: 5 outliers final: 4 residues processed: 21 average time/residue: 0.5830 time to fit residues: 12.4353 Evaluate side-chains 22 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 155 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 10 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- 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 = 0.3856 r_free = 0.3856 target = 0.139221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.115103 restraints weight = 2707.430| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.27 r_work: 0.3438 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.7051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 1425 Z= 0.115 Angle : 0.533 9.024 1914 Z= 0.277 Chirality : 0.041 0.129 217 Planarity : 0.004 0.026 241 Dihedral : 4.060 27.420 190 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.29 % Allowed : 28.29 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 aren not related in a simple way. whole: 0.65 (0.66), residues: 173 helix: 1.49 (0.81), residues: 41 sheet: -2.03 (1.16), residues: 18 loop : 0.60 (0.62), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 134 TYR 0.006 0.001 TYR A 105 PHE 0.003 0.001 PHE A 47 TRP 0.001 0.000 TRP A 9 HIS 0.002 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 1425) covalent geometry : angle 0.53335 ( 1914) hydrogen bonds : bond 0.04560 ( 41) hydrogen bonds : angle 6.01783 ( 114) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 931.10 seconds wall clock time: 16 minutes 45.21 seconds (1005.21 seconds total)