Starting phenix.real_space_refine on Fri May 9 12:42:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z93_39853/05_2025/8z93_39853.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z93_39853/05_2025/8z93_39853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z93_39853/05_2025/8z93_39853.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z93_39853/05_2025/8z93_39853.map" model { file = "/net/cci-nas-00/data/ceres_data/8z93_39853/05_2025/8z93_39853.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z93_39853/05_2025/8z93_39853.cif" } resolution = 4.65 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= 0.002 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 3 5.16 5 C 309 2.51 5 N 69 2.21 5 O 96 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 477 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 159 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Restraints were copied for chains: C, B Time building chain proxies: 0.54, per 1000 atoms: 1.13 Number of scatterers: 477 At special positions: 0 Unit cell: (43.46, 40.28, 29.68, 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 3 16.00 O 96 8.00 N 69 7.00 C 309 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: 0.12 Conformation dependent library (CDL) restraints added in 56.5 milliseconds 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 102 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... No hydrogen bonds 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: 0.00 Time building geometry restraints manager: 0.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 132 1.33 - 1.45: 105 1.45 - 1.56: 243 1.56 - 1.67: 0 1.67 - 1.79: 6 Bond restraints: 486 Sorted by residual: bond pdb=" CA MET C 547 " pdb=" CB MET C 547 " ideal model delta sigma weight residual 1.534 1.517 0.017 1.64e-02 3.72e+03 1.05e+00 bond pdb=" CA MET A 547 " pdb=" CB MET A 547 " ideal model delta sigma weight residual 1.534 1.517 0.016 1.64e-02 3.72e+03 1.00e+00 bond pdb=" CA MET B 547 " pdb=" CB MET B 547 " ideal model delta sigma weight residual 1.534 1.518 0.016 1.64e-02 3.72e+03 9.55e-01 bond pdb=" N THR A 537 " pdb=" CA THR A 537 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.20e-02 6.94e+03 8.04e-01 bond pdb=" N THR C 537 " pdb=" CA THR C 537 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.20e-02 6.94e+03 8.02e-01 ... (remaining 481 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 557 1.30 - 2.59: 82 2.59 - 3.88: 15 3.88 - 5.18: 0 5.18 - 6.47: 3 Bond angle restraints: 657 Sorted by residual: angle pdb=" CA TYR A 534 " pdb=" CB TYR A 534 " pdb=" CG TYR A 534 " ideal model delta sigma weight residual 113.90 120.37 -6.47 1.80e+00 3.09e-01 1.29e+01 angle pdb=" CA TYR C 534 " pdb=" CB TYR C 534 " pdb=" CG TYR C 534 " ideal model delta sigma weight residual 113.90 120.36 -6.46 1.80e+00 3.09e-01 1.29e+01 angle pdb=" CA TYR B 534 " pdb=" CB TYR B 534 " pdb=" CG TYR B 534 " ideal model delta sigma weight residual 113.90 120.34 -6.44 1.80e+00 3.09e-01 1.28e+01 angle pdb=" N GLY C 538 " pdb=" CA GLY C 538 " pdb=" C GLY C 538 " ideal model delta sigma weight residual 111.62 115.43 -3.81 1.77e+00 3.19e-01 4.62e+00 angle pdb=" N GLY A 538 " pdb=" CA GLY A 538 " pdb=" C GLY A 538 " ideal model delta sigma weight residual 111.62 115.41 -3.79 1.77e+00 3.19e-01 4.59e+00 ... (remaining 652 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 6.58: 178 6.58 - 13.15: 26 13.15 - 19.72: 39 19.72 - 26.29: 15 26.29 - 32.86: 9 Dihedral angle restraints: 267 sinusoidal: 96 harmonic: 171 Sorted by residual: dihedral pdb=" CA THR B 537 " pdb=" C THR B 537 " pdb=" N GLY B 538 " pdb=" CA GLY B 538 " ideal model delta harmonic sigma weight residual -180.00 -152.16 -27.84 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA THR C 537 " pdb=" C THR C 537 " pdb=" N GLY C 538 " pdb=" CA GLY C 538 " ideal model delta harmonic sigma weight residual 180.00 -152.17 -27.83 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA THR A 537 " pdb=" C THR A 537 " pdb=" N GLY A 538 " pdb=" CA GLY A 538 " ideal model delta harmonic sigma weight residual 180.00 -152.20 -27.80 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 264 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.038: 36 0.038 - 0.075: 18 0.075 - 0.112: 9 0.112 - 0.148: 3 0.148 - 0.185: 3 Chirality restraints: 69 Sorted by residual: chirality pdb=" CA TYR C 534 " pdb=" N TYR C 534 " pdb=" C TYR C 534 " pdb=" CB TYR C 534 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.19 2.00e-01 2.50e+01 8.59e-01 chirality pdb=" CA TYR B 534 " pdb=" N TYR B 534 " pdb=" C TYR B 534 " pdb=" CB TYR B 534 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.41e-01 chirality pdb=" CA TYR A 534 " pdb=" N TYR A 534 " pdb=" C TYR A 534 " pdb=" CB TYR A 534 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.38e-01 ... (remaining 66 not shown) Planarity restraints: 81 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 534 " 0.017 2.00e-02 2.50e+03 1.46e-02 4.25e+00 pdb=" CG TYR B 534 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR B 534 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR B 534 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 534 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 534 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 534 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 534 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 534 " 0.016 2.00e-02 2.50e+03 1.45e-02 4.23e+00 pdb=" CG TYR A 534 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR A 534 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 534 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 534 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 534 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 534 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 534 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 534 " 0.016 2.00e-02 2.50e+03 1.45e-02 4.22e+00 pdb=" CG TYR C 534 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR C 534 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR C 534 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR C 534 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C 534 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR C 534 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 534 " -0.001 2.00e-02 2.50e+03 ... (remaining 78 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 27 2.63 - 3.20: 532 3.20 - 3.76: 702 3.76 - 4.33: 996 4.33 - 4.90: 1471 Nonbonded interactions: 3728 Sorted by model distance: nonbonded pdb=" N TYR B 531 " pdb=" OG1 THR C 532 " model vdw 2.060 3.120 nonbonded pdb=" N GLY B 550 " pdb=" O ILE C 549 " model vdw 2.232 3.120 nonbonded pdb=" O SER A 536 " pdb=" OG1 THR A 537 " model vdw 2.312 3.040 nonbonded pdb=" O SER C 536 " pdb=" OG1 THR C 537 " model vdw 2.313 3.040 nonbonded pdb=" O SER B 536 " pdb=" OG1 THR B 537 " model vdw 2.313 3.040 ... (remaining 3723 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set refine NCS operators NCS operators will be refined. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 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: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.940 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6203 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 486 Z= 0.307 Angle : 1.053 6.472 657 Z= 0.609 Chirality : 0.065 0.185 69 Planarity : 0.005 0.015 81 Dihedral : 13.343 32.863 165 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 54.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 38.89 % Favored : 61.11 % Rotamer: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -7.84 (0.52), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.97 (0.40), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.036 0.004 TYR A 534 Details of bonding type rmsd covalent geometry : bond 0.00639 ( 486) covalent geometry : angle 1.05252 ( 657) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.018 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0785 time to fit residues: 0.5932 Evaluate side-chains 4 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.0070 overall best weight: 3.3350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 545 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.128854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.114884 restraints weight = 542.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.116893 restraints weight = 297.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.118710 restraints weight = 221.613| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5270 moved from start: 0.6359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 486 Z= 0.346 Angle : 1.032 5.126 657 Z= 0.586 Chirality : 0.082 0.195 69 Planarity : 0.008 0.018 81 Dihedral : 11.181 27.786 69 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 45.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 38.89 % Favored : 61.11 % Rotamer: Outliers : 0.00 % Allowed : 18.75 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -8.37 (0.44), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.37 (0.34), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.043 0.006 TYR C 544 Details of bonding type rmsd covalent geometry : bond 0.00744 ( 486) covalent geometry : angle 1.03234 ( 657) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.019 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0742 time to fit residues: 0.4102 Evaluate side-chains 5 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 overall best weight: 3.6657 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.135787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.116586 restraints weight = 399.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.119243 restraints weight = 242.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.120736 restraints weight = 176.708| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5423 moved from start: 0.7052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 486 Z= 0.259 Angle : 0.973 5.932 657 Z= 0.545 Chirality : 0.078 0.159 69 Planarity : 0.006 0.012 81 Dihedral : 9.887 25.254 69 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 34.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 38.89 % Favored : 61.11 % Rotamer: Outliers : 6.25 % Allowed : 6.25 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -8.15 (0.47), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.20 (0.36), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.024 0.004 TYR C 534 Details of bonding type rmsd covalent geometry : bond 0.00521 ( 486) covalent geometry : angle 0.97282 ( 657) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 4 time to evaluate : 0.017 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 5 average time/residue: 0.0791 time to fit residues: 0.4336 Evaluate side-chains 4 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.0270 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 0.0270 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.6843 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.185613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.163319 restraints weight = 360.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.167080 restraints weight = 183.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.169569 restraints weight = 111.518| |-----------------------------------------------------------------------------| r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5176 moved from start: 0.8127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 486 Z= 0.286 Angle : 0.990 6.833 657 Z= 0.561 Chirality : 0.081 0.202 69 Planarity : 0.006 0.013 81 Dihedral : 8.314 18.683 69 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 34.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 50.00 % Favored : 50.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -8.18 (0.48), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.23 (0.37), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.028 0.004 TYR C 544 Details of bonding type rmsd covalent geometry : bond 0.00634 ( 486) covalent geometry : angle 0.98984 ( 657) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 6 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.019 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0706 time to fit residues: 0.4659 Evaluate side-chains 4 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.0040 overall best weight: 0.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.247029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.216406 restraints weight = 303.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.219286 restraints weight = 144.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.221538 restraints weight = 95.663| |-----------------------------------------------------------------------------| r_work (final): 0.4428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4800 moved from start: 0.7716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 486 Z= 0.143 Angle : 0.784 5.368 657 Z= 0.438 Chirality : 0.066 0.141 69 Planarity : 0.005 0.010 81 Dihedral : 6.426 16.613 69 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 39.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 33.33 % Favored : 66.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -7.96 (0.49), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.06 (0.37), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.025 0.003 TYR B 534 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 486) covalent geometry : angle 0.78442 ( 657) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.018 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0680 time to fit residues: 0.3761 Evaluate side-chains 4 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.152033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.129836 restraints weight = 368.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.132705 restraints weight = 224.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.134863 restraints weight = 166.014| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5638 moved from start: 0.7666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 486 Z= 0.220 Angle : 0.811 5.360 657 Z= 0.464 Chirality : 0.065 0.149 69 Planarity : 0.005 0.012 81 Dihedral : 7.956 20.597 69 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 37.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 38.89 % Favored : 61.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -7.75 (0.46), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.90 (0.35), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.025 0.003 TYR B 534 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 486) covalent geometry : angle 0.81097 ( 657) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.019 Fit side-chains REVERT: B 534 TYR cc_start: 0.6142 (p90) cc_final: 0.5508 (m-10) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0751 time to fit residues: 0.3376 Evaluate side-chains 4 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 overall best weight: 5.6657 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.214615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.160896 restraints weight = 345.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.162706 restraints weight = 271.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.164092 restraints weight = 225.263| |-----------------------------------------------------------------------------| r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5648 moved from start: 0.8681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.037 486 Z= 0.391 Angle : 1.072 5.423 657 Z= 0.583 Chirality : 0.074 0.155 69 Planarity : 0.006 0.014 81 Dihedral : 10.759 28.109 69 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 40.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 33.33 % Favored : 66.67 % Rotamer: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -7.44 (0.58), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.67 (0.44), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.020 0.003 TYR B 534 Details of bonding type rmsd covalent geometry : bond 0.00786 ( 486) covalent geometry : angle 1.07156 ( 657) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 6 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.017 Fit side-chains REVERT: A 547 MET cc_start: 0.7553 (tmm) cc_final: 0.7258 (ttt) outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0567 time to fit residues: 0.3762 Evaluate side-chains 4 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.2650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.184036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.146969 restraints weight = 386.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.152887 restraints weight = 274.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.156607 restraints weight = 213.010| |-----------------------------------------------------------------------------| r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5530 moved from start: 0.9284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 486 Z= 0.165 Angle : 0.874 6.337 657 Z= 0.461 Chirality : 0.062 0.138 69 Planarity : 0.005 0.012 81 Dihedral : 8.276 20.368 69 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 40.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 38.89 % Favored : 61.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -7.08 (0.62), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.39 (0.48), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.025 0.003 TYR A 534 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 486) covalent geometry : angle 0.87428 ( 657) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.019 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0757 time to fit residues: 0.4187 Evaluate side-chains 4 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.2980 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 0.2980 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.8650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.161539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.138472 restraints weight = 375.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.141563 restraints weight = 247.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.143849 restraints weight = 187.807| |-----------------------------------------------------------------------------| r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5298 moved from start: 0.9705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 486 Z= 0.154 Angle : 0.796 4.476 657 Z= 0.439 Chirality : 0.067 0.139 69 Planarity : 0.004 0.011 81 Dihedral : 6.778 19.535 69 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 39.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 38.89 % Favored : 61.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -6.76 (0.69), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.14 (0.53), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.022 0.002 TYR C 534 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 486) covalent geometry : angle 0.79570 ( 657) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 6 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.020 Fit side-chains REVERT: B 534 TYR cc_start: 0.5957 (p90) cc_final: 0.5274 (m-10) outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0767 time to fit residues: 0.5008 Evaluate side-chains 5 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.0070 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 0.0070 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.0060 overall best weight: 0.0067 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.192338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.167147 restraints weight = 245.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.169864 restraints weight = 161.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.171970 restraints weight = 123.631| |-----------------------------------------------------------------------------| r_work (final): 0.4363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4952 moved from start: 1.0288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 486 Z= 0.148 Angle : 0.797 4.673 657 Z= 0.431 Chirality : 0.070 0.145 69 Planarity : 0.004 0.010 81 Dihedral : 6.171 16.316 69 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 34.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 27.78 % Favored : 72.22 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -6.88 (0.63), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.23 (0.48), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.002 TYR A 534 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 486) covalent geometry : angle 0.79691 ( 657) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 6 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.018 Fit side-chains REVERT: A 534 TYR cc_start: 0.5817 (p90) cc_final: 0.4898 (m-10) outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0673 time to fit residues: 0.4429 Evaluate side-chains 6 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 0.0010 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.0010 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.0060 overall best weight: 0.0027 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.237214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.202969 restraints weight = 264.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.205157 restraints weight = 188.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.206678 restraints weight = 151.165| |-----------------------------------------------------------------------------| r_work (final): 0.4435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4926 moved from start: 1.0673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 486 Z= 0.142 Angle : 0.735 4.955 657 Z= 0.418 Chirality : 0.067 0.141 69 Planarity : 0.003 0.010 81 Dihedral : 5.043 14.671 69 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 29.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 27.78 % Favored : 72.22 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -6.80 (0.65), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.18 (0.49), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.002 TYR A 534 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 486) covalent geometry : angle 0.73482 ( 657) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 501.88 seconds wall clock time: 9 minutes 24.10 seconds (564.10 seconds total)