Starting phenix.real_space_refine on Wed Mar 5 14:17:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3jbs_6478/03_2025/3jbs_6478.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jbs_6478/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/3jbs_6478/03_2025/3jbs_6478.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jbs_6478/03_2025/3jbs_6478.map" model { file = "/net/cci-nas-00/data/ceres_data/3jbs_6478/03_2025/3jbs_6478.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jbs_6478/03_2025/3jbs_6478.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 2.22, per 1000 atoms: 1.58 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: 0.47 Conformation dependent library (CDL) restraints added in 224.2 milliseconds 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: 0.18 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: 0.48 Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 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: 1.910 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 12.060 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 27.730 ------------------------------------------------------------------------------- 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= 0.671 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.005 TRP A 9 HIS 0.006 0.002 HIS A 57 PHE 0.020 0.004 PHE A 101 TYR 0.024 0.005 TYR A 54 ARG 0.002 0.000 ARG A 134 *********************** 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 : 0.177 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: 1.6701 time to fit residues: 92.7664 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 : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 14 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3980 r_free = 0.3980 target = 0.150025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.124460 restraints weight = 2692.090| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.43 r_work: 0.3564 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1425 Z= 0.180 Angle : 0.550 4.014 1914 Z= 0.295 Chirality : 0.043 0.127 217 Planarity : 0.005 0.033 241 Dihedral : 4.072 28.139 190 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.95 % Allowed : 15.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.64), residues: 173 helix: 1.90 (0.75), residues: 45 sheet: -1.44 (1.35), residues: 10 loop : 1.02 (0.59), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 9 HIS 0.001 0.000 HIS A 172 PHE 0.005 0.001 PHE A 122 TYR 0.005 0.001 TYR A 158 ARG 0.003 0.001 ARG A 134 *********************** 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 36 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.150 Fit side-chains REVERT: A 82 ARG cc_start: 0.8413 (mmt180) cc_final: 0.7077 (mtt180) REVERT: A 91 VAL cc_start: 0.7800 (t) cc_final: 0.7365 (m) REVERT: A 108 LYS cc_start: 0.1965 (mttt) cc_final: 0.0813 (tptm) REVERT: A 122 PHE cc_start: 0.5761 (OUTLIER) cc_final: 0.5333 (m-80) REVERT: A 136 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7381 (mm-30) REVERT: A 146 ILE cc_start: 0.8462 (mt) cc_final: 0.8247 (mt) outliers start: 6 outliers final: 1 residues processed: 33 average time/residue: 1.0109 time to fit residues: 33.9991 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 : 0.170 ------------------------------------------------------------------------------- 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 12 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.3880 r_free = 0.3880 target = 0.141218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.117231 restraints weight = 2650.069| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.22 r_work: 0.3456 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.5520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 1425 Z= 0.233 Angle : 0.545 5.125 1914 Z= 0.281 Chirality : 0.042 0.122 217 Planarity : 0.005 0.030 241 Dihedral : 4.137 25.275 190 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 5.26 % Allowed : 22.37 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.65), residues: 173 helix: 1.77 (0.76), residues: 45 sheet: -1.99 (1.17), residues: 18 loop : 1.05 (0.63), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 9 HIS 0.001 0.001 HIS A 57 PHE 0.004 0.001 PHE A 47 TYR 0.008 0.001 TYR A 83 ARG 0.003 0.001 ARG A 134 *********************** 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 31 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 23 time to evaluate : 0.192 Fit side-chains REVERT: A 5 LYS cc_start: 0.4822 (mttp) cc_final: 0.4281 (mttt) REVERT: A 82 ARG cc_start: 0.8614 (mmt180) cc_final: 0.6903 (mtt180) REVERT: A 108 LYS cc_start: 0.3221 (mttt) cc_final: 0.1105 (tptm) REVERT: A 122 PHE cc_start: 0.5486 (OUTLIER) cc_final: 0.4876 (m-80) REVERT: A 136 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7401 (mm-30) outliers start: 8 outliers final: 5 residues processed: 29 average time/residue: 1.1806 time to fit residues: 34.8435 Evaluate side-chains 26 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 89 THR 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 4 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 0.4980 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 = 0.3869 r_free = 0.3869 target = 0.139651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.115810 restraints weight = 2690.152| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.23 r_work: 0.3445 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.5969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 1425 Z= 0.191 Angle : 0.524 5.493 1914 Z= 0.271 Chirality : 0.043 0.121 217 Planarity : 0.004 0.025 241 Dihedral : 4.090 27.624 190 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 6.58 % Allowed : 22.37 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.65), residues: 173 helix: 1.13 (0.72), residues: 45 sheet: -1.93 (1.23), residues: 18 loop : 1.02 (0.63), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP A 9 HIS 0.002 0.001 HIS A 57 PHE 0.005 0.001 PHE A 47 TYR 0.006 0.001 TYR A 105 ARG 0.002 0.000 ARG A 51 *********************** 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 35 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 25 time to evaluate : 0.184 Fit side-chains REVERT: A 5 LYS cc_start: 0.4819 (mttp) cc_final: 0.4283 (mttt) REVERT: A 60 ASP cc_start: 0.8048 (p0) cc_final: 0.7510 (p0) REVERT: A 82 ARG cc_start: 0.8632 (mmt180) cc_final: 0.6851 (mtt180) REVERT: A 108 LYS cc_start: 0.3410 (mttt) cc_final: 0.1230 (tptm) REVERT: A 122 PHE cc_start: 0.5414 (OUTLIER) cc_final: 0.4799 (m-80) REVERT: A 136 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7389 (mm-30) outliers start: 10 outliers final: 3 residues processed: 30 average time/residue: 1.1044 time to fit residues: 33.7628 Evaluate side-chains 26 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 89 THR 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 14 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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 = 0.3831 r_free = 0.3831 target = 0.137050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.113250 restraints weight = 2643.745| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.17 r_work: 0.3402 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.6584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 1425 Z= 0.250 Angle : 0.555 5.689 1914 Z= 0.285 Chirality : 0.043 0.123 217 Planarity : 0.004 0.026 241 Dihedral : 4.248 24.081 190 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 7.24 % Allowed : 24.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.64), residues: 173 helix: 1.58 (0.79), residues: 39 sheet: -1.83 (1.25), residues: 18 loop : 0.75 (0.59), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 9 HIS 0.002 0.001 HIS A 57 PHE 0.005 0.001 PHE A 47 TYR 0.009 0.002 TYR A 105 ARG 0.003 0.001 ARG A 134 *********************** 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 34 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 23 time to evaluate : 0.173 Fit side-chains REVERT: A 5 LYS cc_start: 0.5039 (mttp) cc_final: 0.4625 (mttt) REVERT: A 28 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8290 (tt0) REVERT: A 60 ASP cc_start: 0.8214 (p0) cc_final: 0.7638 (p0) REVERT: A 82 ARG cc_start: 0.8705 (mmt180) cc_final: 0.6804 (mtt180) REVERT: A 108 LYS cc_start: 0.3077 (mttt) cc_final: 0.0970 (tptm) REVERT: A 111 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7208 (pp) REVERT: A 122 PHE cc_start: 0.5418 (OUTLIER) cc_final: 0.4789 (m-80) REVERT: A 136 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7257 (mm-30) outliers start: 11 outliers final: 5 residues processed: 29 average time/residue: 1.1160 time to fit residues: 33.0013 Evaluate side-chains 28 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 28 GLN Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 111 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 4 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 16 optimal weight: 0.0270 chunk 11 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 overall best weight: 3.0046 ------------------------------------------------------------------------------- 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 = 0.3823 r_free = 0.3823 target = 0.136552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.112970 restraints weight = 2693.936| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.19 r_work: 0.3396 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.6858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 1425 Z= 0.236 Angle : 0.550 5.882 1914 Z= 0.281 Chirality : 0.044 0.167 217 Planarity : 0.004 0.023 241 Dihedral : 4.358 25.855 190 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 7.24 % Allowed : 23.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.64), residues: 173 helix: 1.35 (0.80), residues: 39 sheet: -1.85 (1.20), residues: 18 loop : 0.70 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 9 HIS 0.003 0.001 HIS A 57 PHE 0.005 0.001 PHE A 47 TYR 0.008 0.001 TYR A 105 ARG 0.002 0.000 ARG A 51 *********************** 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 31 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 20 time to evaluate : 0.171 Fit side-chains REVERT: A 5 LYS cc_start: 0.5049 (mttp) cc_final: 0.4540 (mttt) REVERT: A 28 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8402 (tt0) REVERT: A 60 ASP cc_start: 0.8321 (p0) cc_final: 0.8045 (p0) REVERT: A 82 ARG cc_start: 0.8773 (mmt180) cc_final: 0.6876 (mtt180) REVERT: A 108 LYS cc_start: 0.3278 (mttt) cc_final: 0.0965 (tptm) REVERT: A 111 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.7037 (pp) REVERT: A 117 LYS cc_start: 0.6491 (OUTLIER) cc_final: 0.5964 (mttt) REVERT: A 122 PHE cc_start: 0.5617 (OUTLIER) cc_final: 0.4933 (m-80) REVERT: A 136 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7207 (mm-30) outliers start: 11 outliers final: 5 residues processed: 28 average time/residue: 1.2464 time to fit residues: 35.5234 Evaluate side-chains 28 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 19 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 28 GLN Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 122 PHE 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 4 optimal weight: 8.9990 chunk 9 optimal weight: 30.0000 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.136164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.113061 restraints weight = 2674.737| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.18 r_work: 0.3395 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.7022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1425 Z= 0.241 Angle : 0.565 6.253 1914 Z= 0.291 Chirality : 0.043 0.144 217 Planarity : 0.004 0.024 241 Dihedral : 4.372 24.779 190 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 7.89 % Allowed : 23.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.65), residues: 173 helix: 1.13 (0.81), residues: 39 sheet: -1.86 (1.22), residues: 18 loop : 0.61 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP A 9 HIS 0.002 0.001 HIS A 57 PHE 0.005 0.001 PHE A 47 TYR 0.008 0.001 TYR A 105 ARG 0.002 0.000 ARG A 51 *********************** 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 31 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 19 time to evaluate : 0.162 Fit side-chains REVERT: A 5 LYS cc_start: 0.5063 (mttp) cc_final: 0.4609 (mttt) REVERT: A 28 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8450 (tt0) REVERT: A 60 ASP cc_start: 0.8324 (p0) cc_final: 0.8062 (p0) REVERT: A 82 ARG cc_start: 0.8801 (mmt180) cc_final: 0.6887 (mtt180) REVERT: A 108 LYS cc_start: 0.3041 (mttt) cc_final: 0.0819 (tptm) REVERT: A 111 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.7058 (pp) REVERT: A 117 LYS cc_start: 0.6425 (OUTLIER) cc_final: 0.6064 (mtmt) REVERT: A 122 PHE cc_start: 0.5642 (OUTLIER) cc_final: 0.4969 (m-80) REVERT: A 124 GLU cc_start: 0.4796 (mm-30) cc_final: 0.3703 (pt0) REVERT: A 136 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7304 (mm-30) outliers start: 12 outliers final: 5 residues processed: 27 average time/residue: 1.1083 time to fit residues: 30.5384 Evaluate side-chains 28 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 19 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 28 GLN Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 117 LYS 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 15 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 1 optimal weight: 0.0870 chunk 3 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 overall best weight: 2.0164 ------------------------------------------------------------------------------- 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 = 0.3833 r_free = 0.3833 target = 0.137452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.113933 restraints weight = 2709.937| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.22 r_work: 0.3412 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.7090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1425 Z= 0.191 Angle : 0.534 6.729 1914 Z= 0.274 Chirality : 0.042 0.131 217 Planarity : 0.004 0.024 241 Dihedral : 4.258 26.199 190 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 5.26 % Allowed : 25.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.65), residues: 173 helix: 1.21 (0.82), residues: 39 sheet: -1.91 (1.19), residues: 18 loop : 0.65 (0.61), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP A 9 HIS 0.003 0.001 HIS A 57 PHE 0.004 0.001 PHE A 47 TYR 0.006 0.001 TYR A 105 ARG 0.001 0.000 ARG A 134 *********************** 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 26 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 18 time to evaluate : 0.231 Fit side-chains REVERT: A 5 LYS cc_start: 0.4984 (mttp) cc_final: 0.4380 (mttt) REVERT: A 28 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8478 (tt0) REVERT: A 60 ASP cc_start: 0.8337 (p0) cc_final: 0.8040 (p0) REVERT: A 82 ARG cc_start: 0.8801 (mmt180) cc_final: 0.6931 (mtt180) REVERT: A 108 LYS cc_start: 0.2975 (mttt) cc_final: 0.0983 (tptm) REVERT: A 117 LYS cc_start: 0.6342 (OUTLIER) cc_final: 0.5995 (mtmt) REVERT: A 122 PHE cc_start: 0.5720 (OUTLIER) cc_final: 0.5061 (m-80) REVERT: A 124 GLU cc_start: 0.4977 (mm-30) cc_final: 0.3737 (pt0) REVERT: A 136 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7270 (mm-30) REVERT: A 150 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7868 (mptp) outliers start: 8 outliers final: 4 residues processed: 23 average time/residue: 1.3083 time to fit residues: 30.7041 Evaluate side-chains 26 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 18 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 28 GLN Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 150 LYS 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 0 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.134649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.110740 restraints weight = 2677.279| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.24 r_work: 0.3367 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.7319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 1425 Z= 0.321 Angle : 0.617 7.162 1914 Z= 0.319 Chirality : 0.045 0.132 217 Planarity : 0.005 0.035 241 Dihedral : 4.583 22.813 190 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 6.58 % Allowed : 25.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.65), residues: 173 helix: 0.92 (0.83), residues: 39 sheet: -1.97 (1.22), residues: 18 loop : 0.49 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 9 HIS 0.002 0.001 HIS A 57 PHE 0.005 0.001 PHE A 47 TYR 0.011 0.002 TYR A 105 ARG 0.003 0.001 ARG A 51 *********************** 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 29 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 19 time to evaluate : 0.177 Fit side-chains REVERT: A 5 LYS cc_start: 0.5034 (mttp) cc_final: 0.4578 (mttt) REVERT: A 28 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8868 (tm-30) REVERT: A 60 ASP cc_start: 0.8477 (p0) cc_final: 0.8146 (p0) REVERT: A 82 ARG cc_start: 0.8826 (mmt180) cc_final: 0.6884 (mtt180) REVERT: A 108 LYS cc_start: 0.3231 (mttt) cc_final: 0.0915 (tptm) REVERT: A 117 LYS cc_start: 0.6228 (OUTLIER) cc_final: 0.5832 (mttt) REVERT: A 122 PHE cc_start: 0.5948 (OUTLIER) cc_final: 0.5242 (m-80) REVERT: A 136 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7499 (mm-30) outliers start: 10 outliers final: 4 residues processed: 26 average time/residue: 1.1310 time to fit residues: 29.9849 Evaluate side-chains 26 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 19 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 28 GLN Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 117 LYS 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 6 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 16 optimal weight: 0.0570 chunk 2 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 overall best weight: 1.9904 ------------------------------------------------------------------------------- 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 = 0.3827 r_free = 0.3827 target = 0.136837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.113645 restraints weight = 2698.657| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.19 r_work: 0.3410 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.7363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 1425 Z= 0.198 Angle : 0.574 8.907 1914 Z= 0.293 Chirality : 0.042 0.128 217 Planarity : 0.004 0.024 241 Dihedral : 4.382 26.768 190 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.95 % Allowed : 28.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.66), residues: 173 helix: 1.06 (0.84), residues: 39 sheet: -1.90 (1.17), residues: 18 loop : 0.57 (0.61), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 9 HIS 0.003 0.002 HIS A 57 PHE 0.004 0.001 PHE A 163 TYR 0.006 0.001 TYR A 105 ARG 0.001 0.000 ARG A 134 ********************** 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 24 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 18 time to evaluate : 0.195 Fit side-chains REVERT: A 5 LYS cc_start: 0.4960 (mttp) cc_final: 0.4431 (mttt) REVERT: A 28 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8768 (tm-30) REVERT: A 60 ASP cc_start: 0.8412 (p0) cc_final: 0.8121 (p0) REVERT: A 82 ARG cc_start: 0.8766 (mmt180) cc_final: 0.6943 (mtt180) REVERT: A 108 LYS cc_start: 0.3050 (mttt) cc_final: 0.1059 (tptm) REVERT: A 117 LYS cc_start: 0.6174 (ttmt) cc_final: 0.5815 (mttt) REVERT: A 122 PHE cc_start: 0.5829 (OUTLIER) cc_final: 0.5116 (m-80) REVERT: A 136 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7274 (mm-30) outliers start: 6 outliers final: 3 residues processed: 22 average time/residue: 1.2411 time to fit residues: 27.8582 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 : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 28 GLN Chi-restraints excluded: chain A residue 89 THR 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 4 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 9 optimal weight: 30.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3827 r_free = 0.3827 target = 0.136768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.113399 restraints weight = 2652.745| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.18 r_work: 0.3410 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.7391 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= 0.199 Angle : 0.568 8.891 1914 Z= 0.290 Chirality : 0.042 0.126 217 Planarity : 0.004 0.025 241 Dihedral : 4.218 25.065 190 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.95 % Allowed : 28.95 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.66), residues: 173 helix: 1.22 (0.85), residues: 39 sheet: -1.82 (1.17), residues: 18 loop : 0.60 (0.61), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 9 HIS 0.003 0.002 HIS A 57 PHE 0.004 0.001 PHE A 47 TYR 0.007 0.001 TYR A 105 ARG 0.002 0.000 ARG A 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1878.95 seconds wall clock time: 32 minutes 46.87 seconds (1966.87 seconds total)