Starting phenix.real_space_refine on Wed Jun 4 09:40:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z94_39854/06_2025/8z94_39854.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z94_39854/06_2025/8z94_39854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z94_39854/06_2025/8z94_39854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z94_39854/06_2025/8z94_39854.map" model { file = "/net/cci-nas-00/data/ceres_data/8z94_39854/06_2025/8z94_39854.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z94_39854/06_2025/8z94_39854.cif" } resolution = 4.56 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 6 5.16 5 C 315 2.51 5 N 84 2.21 5 O 102 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-5710/modules/chem_data/mon_lib" Total number of atoms: 507 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 169 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Chain: "A" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 169 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Chain: "C" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 169 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Time building chain proxies: 1.55, per 1000 atoms: 3.06 Number of scatterers: 507 At special positions: 0 Unit cell: (43.46, 39.22, 31.8, 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 6 16.00 O 102 8.00 N 84 7.00 C 315 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: 0.31 Conformation dependent library (CDL) restraints added in 170.9 milliseconds 120 Ramachandran restraints generated. 60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 120 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: 0.39 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: 0.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 171 1.34 - 1.46: 78 1.46 - 1.57: 255 1.57 - 1.69: 0 1.69 - 1.81: 9 Bond restraints: 513 Sorted by residual: bond pdb=" CB VAL B 458 " pdb=" CG1 VAL B 458 " ideal model delta sigma weight residual 1.521 1.426 0.095 3.30e-02 9.18e+02 8.30e+00 bond pdb=" CA VAL C 458 " pdb=" CB VAL C 458 " ideal model delta sigma weight residual 1.553 1.540 0.013 7.40e-03 1.83e+04 2.94e+00 bond pdb=" CA VAL A 458 " pdb=" CB VAL A 458 " ideal model delta sigma weight residual 1.553 1.541 0.012 7.40e-03 1.83e+04 2.59e+00 bond pdb=" CA ASN B 464 " pdb=" C ASN B 464 " ideal model delta sigma weight residual 1.532 1.519 0.013 9.60e-03 1.09e+04 1.88e+00 bond pdb=" CA ASN A 464 " pdb=" C ASN A 464 " ideal model delta sigma weight residual 1.532 1.519 0.013 9.60e-03 1.09e+04 1.83e+00 ... (remaining 508 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 611 1.78 - 3.55: 61 3.55 - 5.32: 17 5.32 - 7.10: 1 7.10 - 8.87: 6 Bond angle restraints: 696 Sorted by residual: angle pdb=" N VAL B 460 " pdb=" CA VAL B 460 " pdb=" C VAL B 460 " ideal model delta sigma weight residual 110.42 104.63 5.79 9.60e-01 1.09e+00 3.64e+01 angle pdb=" CA TYR C 453 " pdb=" CB TYR C 453 " pdb=" CG TYR C 453 " ideal model delta sigma weight residual 113.90 122.77 -8.87 1.80e+00 3.09e-01 2.43e+01 angle pdb=" CA TYR A 453 " pdb=" CB TYR A 453 " pdb=" CG TYR A 453 " ideal model delta sigma weight residual 113.90 122.74 -8.84 1.80e+00 3.09e-01 2.41e+01 angle pdb=" CA TYR B 453 " pdb=" CB TYR B 453 " pdb=" CG TYR B 453 " ideal model delta sigma weight residual 113.90 122.71 -8.81 1.80e+00 3.09e-01 2.39e+01 angle pdb=" C VAL A 458 " pdb=" CA VAL A 458 " pdb=" CB VAL A 458 " ideal model delta sigma weight residual 111.74 108.09 3.65 9.40e-01 1.13e+00 1.51e+01 ... (remaining 691 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.61: 272 17.61 - 35.21: 27 35.21 - 52.81: 0 52.81 - 70.41: 1 70.41 - 88.01: 3 Dihedral angle restraints: 303 sinusoidal: 114 harmonic: 189 Sorted by residual: dihedral pdb=" CA TYR A 465 " pdb=" C TYR A 465 " pdb=" N LEU A 466 " pdb=" CA LEU A 466 " ideal model delta harmonic sigma weight residual 180.00 -164.15 -15.85 0 5.00e+00 4.00e-02 1.00e+01 dihedral pdb=" CA TYR B 465 " pdb=" C TYR B 465 " pdb=" N LEU B 466 " pdb=" CA LEU B 466 " ideal model delta harmonic sigma weight residual 180.00 -164.15 -15.85 0 5.00e+00 4.00e-02 1.00e+01 dihedral pdb=" CA TYR C 465 " pdb=" C TYR C 465 " pdb=" N LEU C 466 " pdb=" CA LEU C 466 " ideal model delta harmonic sigma weight residual -180.00 -164.17 -15.83 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 300 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 55 0.049 - 0.097: 12 0.097 - 0.146: 10 0.146 - 0.195: 0 0.195 - 0.243: 4 Chirality restraints: 81 Sorted by residual: chirality pdb=" CA TYR B 453 " pdb=" N TYR B 453 " pdb=" C TYR B 453 " pdb=" CB TYR B 453 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA TYR A 453 " pdb=" N TYR A 453 " pdb=" C TYR A 453 " pdb=" CB TYR A 453 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA TYR C 453 " pdb=" N TYR C 453 " pdb=" C TYR C 453 " pdb=" CB TYR C 453 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 78 not shown) Planarity restraints: 90 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 453 " -0.019 2.00e-02 2.50e+03 1.59e-02 5.06e+00 pdb=" CG TYR A 453 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR A 453 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 453 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 453 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 453 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 453 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 453 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 453 " -0.019 2.00e-02 2.50e+03 1.58e-02 4.98e+00 pdb=" CG TYR C 453 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR C 453 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR C 453 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR C 453 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 453 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR C 453 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 453 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 453 " -0.019 2.00e-02 2.50e+03 1.57e-02 4.92e+00 pdb=" CG TYR B 453 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR B 453 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR B 453 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 453 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 453 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 453 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 453 " -0.000 2.00e-02 2.50e+03 ... (remaining 87 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 56 2.68 - 3.24: 661 3.24 - 3.79: 803 3.79 - 4.35: 1154 4.35 - 4.90: 1703 Nonbonded interactions: 4377 Sorted by model distance: nonbonded pdb=" N TYR B 453 " pdb=" O ILE C 452 " model vdw 2.126 3.120 nonbonded pdb=" OG SER C 456 " pdb=" N GLY C 457 " model vdw 2.210 3.120 nonbonded pdb=" OG SER A 456 " pdb=" N GLY A 457 " model vdw 2.211 3.120 nonbonded pdb=" OG SER B 456 " pdb=" N GLY B 457 " model vdw 2.212 3.120 nonbonded pdb=" NE2 GLN B 459 " pdb=" CB LEU B 466 " model vdw 2.241 3.520 ... (remaining 4372 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 'B' selection = chain 'C' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 0.900 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: 0.000 Set scattering table: 0.010 Process input model: 12.080 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:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4737 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 : 0.007 0.095 513 Z= 0.372 Angle : 1.425 8.874 696 Z= 0.941 Chirality : 0.077 0.243 81 Planarity : 0.007 0.021 90 Dihedral : 16.605 88.012 183 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 146.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 45.00 % Favored : 55.00 % Rotamer: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % 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: -7.88 (0.45), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.00 (0.34), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.040 0.007 TYR A 453 Details of bonding type rmsd covalent geometry : bond 0.00748 ( 513) covalent geometry : angle 1.42476 ( 696) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 120 Ramachandran restraints generated. 60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 120 Ramachandran restraints generated. 60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 20 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.015 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0726 time to fit residues: 0.6176 Evaluate side-chains 5 residues out of total 20 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.016 ------------------------------------------------------------------------------- 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: 4.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 0.1980 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.7320 ------------------------------------------------------------------------------- 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 = 0.4353 r_free = 0.4353 target = 0.164254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.141317 restraints weight = 408.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.143187 restraints weight = 238.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.144075 restraints weight = 183.416| |-----------------------------------------------------------------------------| r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4776 moved from start: 1.0109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.059 513 Z= 0.591 Angle : 1.751 9.496 696 Z= 1.040 Chirality : 0.095 0.332 81 Planarity : 0.010 0.032 90 Dihedral : 11.465 26.244 69 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 98.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 45.00 % Favored : 55.00 % Rotamer: Outliers : 0.00 % Allowed : 15.00 % Favored : 85.00 % 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: -8.51 (0.29), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.48 (0.22), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.031 0.006 TYR B 453 Details of bonding type rmsd covalent geometry : bond 0.01100 ( 513) covalent geometry : angle 1.75072 ( 696) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 80 Ramachandran restraints generated. 40 Oldfield, 0 Emsley, 40 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 80 Ramachandran restraints generated. 40 Oldfield, 0 Emsley, 40 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 20 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.022 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0647 time to fit residues: 0.5678 Evaluate side-chains 5 residues out of total 20 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.022 ------------------------------------------------------------------------------- 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: 3.9990 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 0.0050 overall best weight: 0.4670 ------------------------------------------------------------------------------- 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 = 0.4521 r_free = 0.4521 target = 0.181482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.151938 restraints weight = 409.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.155591 restraints weight = 242.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.157159 restraints weight = 177.601| |-----------------------------------------------------------------------------| r_work (final): 0.4267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4595 moved from start: 1.0721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.023 513 Z= 0.325 Angle : 1.469 9.442 696 Z= 0.865 Chirality : 0.077 0.221 81 Planarity : 0.007 0.022 90 Dihedral : 10.864 23.602 69 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 58.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 45.00 % Favored : 55.00 % Rotamer: Outliers : 5.00 % Allowed : 5.00 % Favored : 90.00 % 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: -8.20 (0.34), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.25 (0.26), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.039 0.008 TYR A 453 Details of bonding type rmsd covalent geometry : bond 0.00588 ( 513) covalent geometry : angle 1.46920 ( 696) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 80 Ramachandran restraints generated. 40 Oldfield, 0 Emsley, 40 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 80 Ramachandran restraints generated. 40 Oldfield, 0 Emsley, 40 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 20 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 8 time to evaluate : 0.021 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 9 average time/residue: 0.0589 time to fit residues: 0.5817 Evaluate side-chains 6 residues out of total 20 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 5 time to evaluate : 0.021 ------------------------------------------------------------------------------- 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: 4.9990 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.0270 overall best weight: 0.6743 ------------------------------------------------------------------------------- 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 = 0.4429 r_free = 0.4429 target = 0.172141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.142361 restraints weight = 381.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.145933 restraints weight = 221.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.148167 restraints weight = 160.045| |-----------------------------------------------------------------------------| r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4606 moved from start: 1.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.031 513 Z= 0.366 Angle : 1.528 9.643 696 Z= 0.886 Chirality : 0.076 0.223 81 Planarity : 0.007 0.022 90 Dihedral : 12.256 29.316 69 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 62.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 45.00 % Favored : 55.00 % Rotamer: Outliers : 0.00 % Allowed : 15.00 % Favored : 85.00 % 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: -8.28 (0.38), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.31 (0.29), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.041 0.009 TYR A 453 Details of bonding type rmsd covalent geometry : bond 0.00715 ( 513) covalent geometry : angle 1.52804 ( 696) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 80 Ramachandran restraints generated. 40 Oldfield, 0 Emsley, 40 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 80 Ramachandran restraints generated. 40 Oldfield, 0 Emsley, 40 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 20 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.022 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0651 time to fit residues: 0.5711 Evaluate side-chains 6 residues out of total 20 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.022 ------------------------------------------------------------------------------- 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: 3.9990 chunk 1 optimal weight: 0.0050 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.0050 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.0270 overall best weight: 0.0123 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.194525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.163299 restraints weight = 312.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.167186 restraints weight = 181.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.169759 restraints weight = 130.647| |-----------------------------------------------------------------------------| r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4204 moved from start: 1.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.022 513 Z= 0.302 Angle : 1.393 9.630 696 Z= 0.800 Chirality : 0.072 0.216 81 Planarity : 0.007 0.022 90 Dihedral : 11.977 27.598 69 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 51.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 45.00 % Favored : 55.00 % Rotamer: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -7.85 (0.48), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.98 (0.37), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.040 0.009 TYR A 453 Details of bonding type rmsd covalent geometry : bond 0.00569 ( 513) covalent geometry : angle 1.39286 ( 696) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 80 Ramachandran restraints generated. 40 Oldfield, 0 Emsley, 40 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 80 Ramachandran restraints generated. 40 Oldfield, 0 Emsley, 40 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 20 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.021 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0629 time to fit residues: 0.5527 Evaluate side-chains 7 residues out of total 20 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.022 ------------------------------------------------------------------------------- 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: 4.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.1980 overall best weight: 2.0653 ------------------------------------------------------------------------------- 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 = 0.4315 r_free = 0.4315 target = 0.163407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.139813 restraints weight = 385.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.143050 restraints weight = 243.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.145885 restraints weight = 172.627| |-----------------------------------------------------------------------------| r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4744 moved from start: 1.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.041 513 Z= 0.389 Angle : 1.467 9.663 696 Z= 0.835 Chirality : 0.068 0.240 81 Planarity : 0.007 0.024 90 Dihedral : 12.617 27.484 69 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 60.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 55.00 % Favored : 45.00 % Rotamer: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % 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: -7.84 (0.45), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.97 (0.34), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.043 0.009 TYR C 453 Details of bonding type rmsd covalent geometry : bond 0.00814 ( 513) covalent geometry : angle 1.46683 ( 696) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 80 Ramachandran restraints generated. 40 Oldfield, 0 Emsley, 40 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 80 Ramachandran restraints generated. 40 Oldfield, 0 Emsley, 40 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 20 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.022 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0703 time to fit residues: 0.5405 Evaluate side-chains 6 residues out of total 20 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.021 ------------------------------------------------------------------------------- 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: 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: 0.0040 overall best weight: 0.0060 ------------------------------------------------------------------------------- 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 = 0.4466 r_free = 0.4466 target = 0.175339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.154365 restraints weight = 466.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.157793 restraints weight = 292.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.160125 restraints weight = 206.628| |-----------------------------------------------------------------------------| r_work (final): 0.4301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4484 moved from start: 1.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.021 513 Z= 0.293 Angle : 1.305 9.588 696 Z= 0.750 Chirality : 0.064 0.185 81 Planarity : 0.006 0.019 90 Dihedral : 12.087 29.812 69 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 50.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 40.00 % Favored : 60.00 % Rotamer: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -7.80 (0.42), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.94 (0.32), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.036 0.009 TYR B 453 Details of bonding type rmsd covalent geometry : bond 0.00544 ( 513) covalent geometry : angle 1.30465 ( 696) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 80 Ramachandran restraints generated. 40 Oldfield, 0 Emsley, 40 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 80 Ramachandran restraints generated. 40 Oldfield, 0 Emsley, 40 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 20 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.024 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0626 time to fit residues: 0.4897 Evaluate side-chains 6 residues out of total 20 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.022 ------------------------------------------------------------------------------- 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: 4.9990 chunk 1 optimal weight: 0.2980 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 0.2980 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.5317 ------------------------------------------------------------------------------- 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 = 0.4717 r_free = 0.4717 target = 0.205622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.176276 restraints weight = 3785.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.179290 restraints weight = 2644.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.180564 restraints weight = 2127.515| |-----------------------------------------------------------------------------| r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4301 moved from start: 1.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.020 513 Z= 0.273 Angle : 1.357 9.681 696 Z= 0.762 Chirality : 0.065 0.200 81 Planarity : 0.006 0.020 90 Dihedral : 12.471 29.480 69 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 52.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 50.00 % Favored : 50.00 % Rotamer: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % 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: -7.47 (0.48), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.69 (0.36), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.040 0.009 TYR B 453 Details of bonding type rmsd covalent geometry : bond 0.00517 ( 513) covalent geometry : angle 1.35716 ( 696) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 80 Ramachandran restraints generated. 40 Oldfield, 0 Emsley, 40 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 80 Ramachandran restraints generated. 40 Oldfield, 0 Emsley, 40 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 6 residues out of total 20 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.021 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0603 time to fit residues: 0.4078 Evaluate side-chains 7 residues out of total 20 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.020 ------------------------------------------------------------------------------- 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: 4.9990 chunk 1 optimal weight: 0.0040 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 0.0040 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.3357 ------------------------------------------------------------------------------- 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 = 0.4543 r_free = 0.4543 target = 0.188778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.157194 restraints weight = 385.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.159549 restraints weight = 287.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.161306 restraints weight = 231.655| |-----------------------------------------------------------------------------| r_work (final): 0.4288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4407 moved from start: 1.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 513 Z= 0.269 Angle : 1.318 9.788 696 Z= 0.748 Chirality : 0.064 0.192 81 Planarity : 0.006 0.020 90 Dihedral : 12.008 29.098 69 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 49.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 45.00 % Favored : 55.00 % 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: -7.37 (0.50), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.61 (0.38), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.036 0.009 TYR C 453 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 513) covalent geometry : angle 1.31774 ( 696) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 80 Ramachandran restraints generated. 40 Oldfield, 0 Emsley, 40 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 80 Ramachandran restraints generated. 40 Oldfield, 0 Emsley, 40 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 20 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.022 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0619 time to fit residues: 0.4821 Evaluate side-chains 5 residues out of total 20 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.022 ------------------------------------------------------------------------------- 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: 5.9990 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.7313 ------------------------------------------------------------------------------- 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 = 0.4422 r_free = 0.4422 target = 0.199929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.162439 restraints weight = 305.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.164560 restraints weight = 225.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.166695 restraints weight = 192.229| |-----------------------------------------------------------------------------| r_work (final): 0.4711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4453 moved from start: 1.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.019 513 Z= 0.251 Angle : 1.314 9.994 696 Z= 0.746 Chirality : 0.066 0.201 81 Planarity : 0.006 0.020 90 Dihedral : 12.177 30.936 69 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 48.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 50.00 % Favored : 50.00 % Rotamer: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.76 % 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: -7.26 (0.45), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.53 (0.34), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.045 0.009 TYR C 453 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 513) covalent geometry : angle 1.31418 ( 696) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 80 Ramachandran restraints generated. 40 Oldfield, 0 Emsley, 40 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 80 Ramachandran restraints generated. 40 Oldfield, 0 Emsley, 40 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 20 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.022 Fit side-chains REVERT: A 451 ASN cc_start: 0.7839 (m110) cc_final: 0.7500 (t0) outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0596 time to fit residues: 0.5256 Evaluate side-chains 8 residues out of total 20 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.021 ------------------------------------------------------------------------------- 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: 5.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 overall best weight: 1.5987 ------------------------------------------------------------------------------- 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 = 0.4765 r_free = 0.4765 target = 0.205636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.179122 restraints weight = 415.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.179117 restraints weight = 438.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.179117 restraints weight = 438.421| |-----------------------------------------------------------------------------| r_work (final): 0.4885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4763 moved from start: 1.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 513 Z= 0.311 Angle : 1.415 10.036 696 Z= 0.804 Chirality : 0.065 0.216 81 Planarity : 0.007 0.021 90 Dihedral : 13.030 32.659 69 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 61.62 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 : 4.76 % 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: -6.84 (0.58), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.21 (0.44), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.050 0.010 TYR A 453 Details of bonding type rmsd covalent geometry : bond 0.00639 ( 513) covalent geometry : angle 1.41538 ( 696) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 561.33 seconds wall clock time: 11 minutes 35.54 seconds (695.54 seconds total)