Starting phenix.real_space_refine on Mon Feb 10 19:27:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3jbs_6478/02_2025/3jbs_6478.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jbs_6478/02_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_6478/02_2025/3jbs_6478.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jbs_6478/02_2025/3jbs_6478.map" model { file = "/net/cci-nas-00/data/ceres_data/3jbs_6478/02_2025/3jbs_6478.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jbs_6478/02_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-5592/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: 2.25, per 1000 atoms: 1.61 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: 0.35 Conformation dependent library (CDL) restraints added in 170.1 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: 0.16 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: 0.27 Time building geometry restraints manager: 0.40 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: 1.750 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 9.850 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:13.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.000 ------------------------------------------------------------------------------- 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 : 0.178 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: 1.6866 time to fit residues: 93.6903 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 : 0.230 ------------------------------------------------------------------------------- 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: 0.7980 chunk 6 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A 57 HIS A 167 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.147917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.123428 restraints weight = 2714.029| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.29 r_work: 0.3540 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 1425 Z= 0.195 Angle : 0.563 4.373 1914 Z= 0.301 Chirality : 0.043 0.127 217 Planarity : 0.005 0.035 241 Dihedral : 4.094 27.300 190 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.29 % Allowed : 16.45 % 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: 1.52 (0.63), residues: 173 helix: 1.92 (0.75), residues: 45 sheet: -1.38 (1.38), residues: 10 loop : 1.04 (0.59), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 9 HIS 0.002 0.001 HIS A 172 PHE 0.005 0.001 PHE A 122 TYR 0.007 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 33 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.180 Fit side-chains REVERT: A 9 TRP cc_start: 0.4396 (m-10) cc_final: 0.4187 (m100) REVERT: A 82 ARG cc_start: 0.8701 (mmt180) cc_final: 0.7216 (mtt180) REVERT: A 91 VAL cc_start: 0.8113 (t) cc_final: 0.7672 (m) REVERT: A 108 LYS cc_start: 0.2585 (mttt) cc_final: 0.0649 (tptp) REVERT: A 122 PHE cc_start: 0.5783 (m-80) cc_final: 0.5365 (m-80) REVERT: A 136 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7471 (mm-30) outliers start: 5 outliers final: 1 residues processed: 31 average time/residue: 0.9564 time to fit residues: 30.3302 Evaluate side-chains 29 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 12 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 15 optimal weight: 0.0980 chunk 9 optimal weight: 0.0370 chunk 1 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.8262 ------------------------------------------------------------------------------- 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 = 0.3951 r_free = 0.3951 target = 0.147360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.122006 restraints weight = 2626.458| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.35 r_work: 0.3538 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4904 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= 0.131 Angle : 0.476 5.663 1914 Z= 0.244 Chirality : 0.040 0.123 217 Planarity : 0.004 0.028 241 Dihedral : 3.861 28.974 190 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 3.79 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 (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: 1.35 (0.66), residues: 173 helix: 1.94 (0.76), residues: 45 sheet: -1.99 (1.11), residues: 18 loop : 1.16 (0.63), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 9 HIS 0.002 0.001 HIS A 57 PHE 0.003 0.001 PHE A 47 TYR 0.005 0.001 TYR A 158 ARG 0.003 0.000 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 38 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.157 Fit side-chains REVERT: A 19 LYS cc_start: 0.8162 (mttt) cc_final: 0.7473 (mttp) REVERT: A 82 ARG cc_start: 0.8351 (mmt180) cc_final: 0.6866 (mtt180) REVERT: A 91 VAL cc_start: 0.7964 (t) cc_final: 0.7600 (m) REVERT: A 108 LYS cc_start: 0.2265 (mttt) cc_final: 0.1052 (tptm) REVERT: A 122 PHE cc_start: 0.5289 (OUTLIER) cc_final: 0.4665 (m-80) REVERT: A 136 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7210 (mm-30) REVERT: A 139 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8325 (mtpp) outliers start: 8 outliers final: 4 residues processed: 34 average time/residue: 1.0762 time to fit residues: 37.2531 Evaluate side-chains 29 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.174 ------------------------------------------------------------------------------- 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 139 LYS 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: 4.9990 chunk 11 optimal weight: 5.9990 chunk 2 optimal weight: 0.1980 chunk 6 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 = 0.142716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.117602 restraints weight = 2649.931| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.26 r_work: 0.3466 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 1425 Z= 0.168 Angle : 0.494 4.899 1914 Z= 0.259 Chirality : 0.042 0.124 217 Planarity : 0.004 0.023 241 Dihedral : 3.848 27.148 190 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 5.92 % Allowed : 22.37 % Favored : 71.71 % 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: 0.95 (0.65), residues: 173 helix: 1.33 (0.75), residues: 45 sheet: -2.01 (1.18), residues: 18 loop : 1.00 (0.62), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 9 HIS 0.002 0.001 HIS A 57 PHE 0.004 0.001 PHE A 47 TYR 0.005 0.001 TYR A 83 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 30 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 21 time to evaluate : 0.184 Fit side-chains REVERT: A 82 ARG cc_start: 0.8595 (mmt180) cc_final: 0.6831 (mtt180) REVERT: A 91 VAL cc_start: 0.8224 (t) cc_final: 0.7707 (m) REVERT: A 108 LYS cc_start: 0.3051 (mttt) cc_final: 0.1306 (tptm) REVERT: A 122 PHE cc_start: 0.5405 (OUTLIER) cc_final: 0.4844 (m-80) REVERT: A 124 GLU cc_start: 0.4798 (mm-30) cc_final: 0.3844 (pt0) REVERT: A 136 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7393 (mm-30) outliers start: 9 outliers final: 3 residues processed: 26 average time/residue: 1.0462 time to fit residues: 27.8423 Evaluate side-chains 24 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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 154 LEU 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: 5.9990 chunk 8 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 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 = 0.3838 r_free = 0.3838 target = 0.137410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.112888 restraints weight = 2622.691| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.25 r_work: 0.3403 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.6238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 1425 Z= 0.245 Angle : 0.562 7.492 1914 Z= 0.285 Chirality : 0.043 0.123 217 Planarity : 0.004 0.028 241 Dihedral : 4.231 23.554 190 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 4.48 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: 0.88 (0.65), residues: 173 helix: 1.72 (0.80), residues: 39 sheet: -2.01 (1.25), residues: 18 loop : 0.78 (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 0.006 0.001 PHE A 47 TYR 0.008 0.001 TYR A 105 ARG 0.003 0.001 ARG A 51 *********************** 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 28 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.165 Fit side-chains REVERT: A 5 LYS cc_start: 0.5265 (tppt) cc_final: 0.4618 (mttm) REVERT: A 60 ASP cc_start: 0.8160 (p0) cc_final: 0.7629 (p0) REVERT: A 82 ARG cc_start: 0.8684 (mmt180) cc_final: 0.6791 (mtt180) REVERT: A 108 LYS cc_start: 0.3308 (mttt) cc_final: 0.0697 (tptm) REVERT: A 122 PHE cc_start: 0.5467 (OUTLIER) cc_final: 0.4859 (m-80) REVERT: A 136 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7372 (mm-30) outliers start: 8 outliers final: 5 residues processed: 25 average time/residue: 1.1061 time to fit residues: 28.2488 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 : 0.185 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 4 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 3 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.135300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.111785 restraints weight = 2686.595| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.21 r_work: 0.3384 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.6692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 1425 Z= 0.313 Angle : 0.601 6.038 1914 Z= 0.311 Chirality : 0.044 0.153 217 Planarity : 0.005 0.031 241 Dihedral : 4.500 24.320 190 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 5.26 % Allowed : 26.32 % 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: 0.54 (0.65), residues: 173 helix: 1.36 (0.83), residues: 39 sheet: -1.97 (1.28), residues: 18 loop : 0.54 (0.59), 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 0.006 0.001 PHE A 47 TYR 0.011 0.002 TYR A 105 ARG 0.003 0.001 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 25 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 17 time to evaluate : 0.185 Fit side-chains REVERT: A 5 LYS cc_start: 0.5337 (tppt) cc_final: 0.3999 (mttp) REVERT: A 8 LYS cc_start: 0.7882 (ttmm) cc_final: 0.7661 (tptt) REVERT: A 60 ASP cc_start: 0.8341 (p0) cc_final: 0.8033 (p0) REVERT: A 82 ARG cc_start: 0.8747 (mmt180) cc_final: 0.6850 (mtt180) REVERT: A 108 LYS cc_start: 0.3552 (mttt) cc_final: 0.0958 (tptm) REVERT: A 122 PHE cc_start: 0.5507 (OUTLIER) cc_final: 0.4875 (m-80) REVERT: A 124 GLU cc_start: 0.4792 (mm-30) cc_final: 0.3759 (pt0) REVERT: A 136 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7234 (mm-30) outliers start: 8 outliers final: 5 residues processed: 24 average time/residue: 1.0797 time to fit residues: 26.4789 Evaluate side-chains 22 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 16 time to evaluate : 0.156 ------------------------------------------------------------------------------- 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 4 optimal weight: 0.9990 chunk 9 optimal weight: 0.0570 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- 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 = 0.3851 r_free = 0.3851 target = 0.138840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.115595 restraints weight = 2643.340| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.20 r_work: 0.3435 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.6776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 1425 Z= 0.150 Angle : 0.500 6.489 1914 Z= 0.258 Chirality : 0.041 0.135 217 Planarity : 0.004 0.024 241 Dihedral : 4.167 28.064 190 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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 (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: 0.68 (0.66), residues: 173 helix: 1.48 (0.83), residues: 39 sheet: -1.98 (1.19), residues: 18 loop : 0.65 (0.61), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 9 HIS 0.003 0.001 HIS A 57 PHE 0.004 0.001 PHE A 47 TYR 0.005 0.001 TYR A 105 ARG 0.001 0.000 ARG A 134 *********************** 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 23 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.158 Fit side-chains REVERT: A 5 LYS cc_start: 0.5208 (tppt) cc_final: 0.3893 (mttp) REVERT: A 8 LYS cc_start: 0.7892 (ttmm) cc_final: 0.7683 (tptt) REVERT: A 60 ASP cc_start: 0.8156 (p0) cc_final: 0.7870 (p0) REVERT: A 82 ARG cc_start: 0.8738 (mmt180) cc_final: 0.6886 (mtt180) REVERT: A 108 LYS cc_start: 0.3134 (mttt) cc_final: 0.1221 (tptm) REVERT: A 122 PHE cc_start: 0.5718 (OUTLIER) cc_final: 0.5053 (m-80) REVERT: A 136 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7270 (mm-30) outliers start: 5 outliers final: 3 residues processed: 22 average time/residue: 1.2211 time to fit residues: 27.4014 Evaluate side-chains 22 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.176 ------------------------------------------------------------------------------- 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 15 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 3 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 0.2980 chunk 8 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.3842 r_free = 0.3842 target = 0.138095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.114834 restraints weight = 2712.743| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.24 r_work: 0.3424 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.6846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 1425 Z= 0.189 Angle : 0.515 6.737 1914 Z= 0.268 Chirality : 0.042 0.134 217 Planarity : 0.004 0.024 241 Dihedral : 4.092 25.592 190 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 5.26 % Allowed : 26.32 % 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: 0.62 (0.65), residues: 173 helix: 1.44 (0.84), residues: 39 sheet: -1.96 (1.19), residues: 18 loop : 0.59 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 9 HIS 0.002 0.001 HIS A 57 PHE 0.004 0.001 PHE A 47 TYR 0.006 0.001 TYR A 105 ARG 0.002 0.000 ARG A 51 *********************** 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 : 0.187 Fit side-chains REVERT: A 5 LYS cc_start: 0.5356 (tppt) cc_final: 0.4780 (mttt) REVERT: A 8 LYS cc_start: 0.7900 (ttmm) cc_final: 0.7665 (tptt) REVERT: A 60 ASP cc_start: 0.8243 (p0) cc_final: 0.7957 (p0) REVERT: A 82 ARG cc_start: 0.8790 (mmt180) cc_final: 0.6897 (mtt180) REVERT: A 108 LYS cc_start: 0.3256 (mttt) cc_final: 0.1241 (tptm) REVERT: A 122 PHE cc_start: 0.5756 (OUTLIER) cc_final: 0.5121 (m-80) REVERT: A 124 GLU cc_start: 0.4813 (mm-30) cc_final: 0.3818 (pt0) REVERT: A 136 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7345 (mm-30) outliers start: 8 outliers final: 4 residues processed: 24 average time/residue: 1.1909 time to fit residues: 29.1665 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 : 0.164 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 0 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3848 r_free = 0.3848 target = 0.138665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.115580 restraints weight = 2644.464| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.21 r_work: 0.3434 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.6918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 1425 Z= 0.175 Angle : 0.520 7.376 1914 Z= 0.270 Chirality : 0.042 0.126 217 Planarity : 0.004 0.024 241 Dihedral : 4.071 26.262 190 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.95 % Allowed : 27.63 % 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: 0.64 (0.65), residues: 173 helix: 1.35 (0.83), residues: 39 sheet: -2.03 (1.17), residues: 18 loop : 0.66 (0.61), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 9 HIS 0.002 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 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 22 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 16 time to evaluate : 0.185 Fit side-chains REVERT: A 5 LYS cc_start: 0.5135 (tppt) cc_final: 0.4559 (mttt) REVERT: A 8 LYS cc_start: 0.8021 (ttmm) cc_final: 0.7605 (tptt) REVERT: A 82 ARG cc_start: 0.8790 (mmt180) cc_final: 0.6903 (mtt180) REVERT: A 108 LYS cc_start: 0.3128 (mttt) cc_final: 0.1260 (tptm) REVERT: A 122 PHE cc_start: 0.5850 (OUTLIER) cc_final: 0.5217 (m-80) REVERT: A 124 GLU cc_start: 0.4748 (mm-30) cc_final: 0.3707 (pt0) REVERT: A 136 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7347 (mm-30) outliers start: 6 outliers final: 4 residues processed: 21 average time/residue: 1.1400 time to fit residues: 24.5025 Evaluate side-chains 21 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 16 time to evaluate : 0.178 ------------------------------------------------------------------------------- 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 6 optimal weight: 0.7980 chunk 4 optimal weight: 0.0470 chunk 11 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 2 optimal weight: 0.0670 chunk 0 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 1 optimal weight: 0.0010 overall best weight: 0.3822 ------------------------------------------------------------------------------- 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 = 0.3890 r_free = 0.3890 target = 0.141861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.118966 restraints weight = 2696.300| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.23 r_work: 0.3489 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.6962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 1425 Z= 0.141 Angle : 0.505 7.158 1914 Z= 0.266 Chirality : 0.042 0.129 217 Planarity : 0.004 0.026 241 Dihedral : 3.960 28.551 190 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.63 % Allowed : 28.95 % 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: 0.67 (0.66), residues: 173 helix: 1.11 (0.78), residues: 41 sheet: -2.07 (1.14), residues: 18 loop : 0.81 (0.63), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 9 HIS 0.003 0.001 HIS A 57 PHE 0.003 0.000 PHE A 163 TYR 0.003 0.000 TYR A 105 ARG 0.003 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 21 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.180 Fit side-chains REVERT: A 5 LYS cc_start: 0.5009 (tppt) cc_final: 0.3895 (mttp) REVERT: A 8 LYS cc_start: 0.8034 (ttmm) cc_final: 0.7633 (tptt) REVERT: A 60 ASP cc_start: 0.8165 (p0) cc_final: 0.7929 (p0) REVERT: A 82 ARG cc_start: 0.8813 (mmt180) cc_final: 0.6953 (mtt180) REVERT: A 108 LYS cc_start: 0.2628 (mttt) cc_final: 0.1360 (tptm) REVERT: A 122 PHE cc_start: 0.5758 (OUTLIER) cc_final: 0.5148 (m-80) REVERT: A 124 GLU cc_start: 0.4758 (mm-30) cc_final: 0.3719 (pt0) REVERT: A 136 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7356 (mm-30) outliers start: 4 outliers final: 3 residues processed: 20 average time/residue: 1.1155 time to fit residues: 22.8263 Evaluate side-chains 21 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.178 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 4 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.3848 r_free = 0.3848 target = 0.138771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.115754 restraints weight = 2660.482| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.22 r_work: 0.3442 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.7025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 1425 Z= 0.187 Angle : 0.536 7.429 1914 Z= 0.278 Chirality : 0.043 0.131 217 Planarity : 0.004 0.027 241 Dihedral : 3.937 24.980 190 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % 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: 0.90 (0.66), residues: 173 helix: 1.62 (0.83), residues: 39 sheet: -2.01 (1.16), residues: 18 loop : 0.84 (0.62), 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 0.004 0.001 PHE A 47 TYR 0.006 0.001 TYR A 105 ARG 0.002 0.000 ARG A 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1805.62 seconds wall clock time: 32 minutes 32.81 seconds (1952.81 seconds total)