Starting phenix.real_space_refine on Wed Sep 17 02:56:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7da4_30622/09_2025/7da4_30622.cif Found real_map, /net/cci-nas-00/data/ceres_data/7da4_30622/09_2025/7da4_30622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7da4_30622/09_2025/7da4_30622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7da4_30622/09_2025/7da4_30622.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7da4_30622/09_2025/7da4_30622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7da4_30622/09_2025/7da4_30622.map" } resolution = 4.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 507 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 169 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Restraints were copied for chains: A, C Time building chain proxies: 0.14, per 1000 atoms: 0.28 Number of scatterers: 507 At special positions: 0 Unit cell: (42.4, 38.16, 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 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: 0.02 Conformation dependent library (CDL) restraints added in 14.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.56 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: 0.04 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: 88 1.46 - 1.57: 245 1.57 - 1.69: 0 1.69 - 1.81: 9 Bond restraints: 513 Sorted by residual: bond pdb=" CA ASN A 464 " pdb=" CB ASN A 464 " ideal model delta sigma weight residual 1.530 1.486 0.044 1.69e-02 3.50e+03 6.73e+00 bond pdb=" CA ASN B 464 " pdb=" CB ASN B 464 " ideal model delta sigma weight residual 1.530 1.487 0.044 1.69e-02 3.50e+03 6.68e+00 bond pdb=" CA ASN C 464 " pdb=" CB ASN C 464 " ideal model delta sigma weight residual 1.530 1.487 0.043 1.69e-02 3.50e+03 6.61e+00 bond pdb=" CB VAL B 458 " pdb=" CG1 VAL B 458 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.53e+00 bond pdb=" CB VAL C 458 " pdb=" CG1 VAL C 458 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.49e+00 ... (remaining 508 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 575 1.66 - 3.32: 91 3.32 - 4.98: 12 4.98 - 6.64: 12 6.64 - 8.30: 6 Bond angle restraints: 696 Sorted by residual: angle pdb=" C ASN A 464 " pdb=" N TYR A 465 " pdb=" CA TYR A 465 " ideal model delta sigma weight residual 121.54 129.84 -8.30 1.91e+00 2.74e-01 1.89e+01 angle pdb=" C ASN B 464 " pdb=" N TYR B 465 " pdb=" CA TYR B 465 " ideal model delta sigma weight residual 121.54 129.83 -8.29 1.91e+00 2.74e-01 1.88e+01 angle pdb=" C ASN C 464 " pdb=" N TYR C 465 " pdb=" CA TYR C 465 " ideal model delta sigma weight residual 121.54 129.78 -8.24 1.91e+00 2.74e-01 1.86e+01 angle pdb=" N TYR C 465 " pdb=" CA TYR C 465 " pdb=" CB TYR C 465 " ideal model delta sigma weight residual 110.49 104.05 6.44 1.69e+00 3.50e-01 1.45e+01 angle pdb=" N TYR A 465 " pdb=" CA TYR A 465 " pdb=" CB TYR A 465 " ideal model delta sigma weight residual 110.49 104.09 6.40 1.69e+00 3.50e-01 1.44e+01 ... (remaining 691 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.76: 264 17.76 - 35.52: 36 35.52 - 53.27: 0 53.27 - 71.03: 0 71.03 - 88.78: 3 Dihedral angle restraints: 303 sinusoidal: 114 harmonic: 189 Sorted by residual: dihedral pdb=" CA VAL B 460 " pdb=" C VAL B 460 " pdb=" N GLY B 461 " pdb=" CA GLY B 461 " ideal model delta harmonic sigma weight residual 180.00 154.48 25.52 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA VAL C 460 " pdb=" C VAL C 460 " pdb=" N GLY C 461 " pdb=" CA GLY C 461 " ideal model delta harmonic sigma weight residual 180.00 154.48 25.52 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA VAL A 460 " pdb=" C VAL A 460 " pdb=" N GLY A 461 " pdb=" CA GLY A 461 " ideal model delta harmonic sigma weight residual 180.00 154.51 25.49 0 5.00e+00 4.00e-02 2.60e+01 ... (remaining 300 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.065: 66 0.065 - 0.129: 12 0.129 - 0.193: 0 0.193 - 0.257: 0 0.257 - 0.321: 3 Chirality restraints: 81 Sorted by residual: chirality pdb=" CA ASN A 464 " pdb=" N ASN A 464 " pdb=" C ASN A 464 " pdb=" CB ASN A 464 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CA ASN C 464 " pdb=" N ASN C 464 " pdb=" C ASN C 464 " pdb=" CB ASN C 464 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CA ASN B 464 " pdb=" N ASN B 464 " pdb=" C ASN B 464 " pdb=" CB ASN B 464 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.51e+00 ... (remaining 78 not shown) Planarity restraints: 90 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 464 " 0.008 2.00e-02 2.50e+03 1.72e-02 2.95e+00 pdb=" C ASN C 464 " -0.030 2.00e-02 2.50e+03 pdb=" O ASN C 464 " 0.011 2.00e-02 2.50e+03 pdb=" N TYR C 465 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 464 " -0.008 2.00e-02 2.50e+03 1.70e-02 2.89e+00 pdb=" C ASN A 464 " 0.029 2.00e-02 2.50e+03 pdb=" O ASN A 464 " -0.011 2.00e-02 2.50e+03 pdb=" N TYR A 465 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 464 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.83e+00 pdb=" C ASN B 464 " 0.029 2.00e-02 2.50e+03 pdb=" O ASN B 464 " -0.011 2.00e-02 2.50e+03 pdb=" N TYR B 465 " -0.010 2.00e-02 2.50e+03 ... (remaining 87 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 158 2.78 - 3.31: 608 3.31 - 3.84: 849 3.84 - 4.37: 978 4.37 - 4.90: 1760 Nonbonded interactions: 4353 Sorted by model distance: nonbonded pdb=" ND2 ASN B 454 " pdb=" O SER B 456 " model vdw 2.245 3.120 nonbonded pdb=" ND2 ASN A 454 " pdb=" O SER A 456 " model vdw 2.246 3.120 nonbonded pdb=" ND2 ASN C 454 " pdb=" O SER C 456 " model vdw 2.247 3.120 nonbonded pdb=" CG ASN B 464 " pdb=" N ASN C 464 " model vdw 2.485 3.350 nonbonded pdb=" N ASN C 463 " pdb=" OD1 ASN C 463 " model vdw 2.497 3.120 ... (remaining 4348 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 'B' selection = chain 'A' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.200 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: 0.010 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 1.800 Find NCS groups from input model: 0.000 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 3.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.053 513 Z= 0.484 Angle : 1.542 8.296 696 Z= 0.836 Chirality : 0.076 0.321 81 Planarity : 0.006 0.017 90 Dihedral : 17.158 88.782 183 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 79.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 50.00 % Favored : 50.00 % Rotamer: Outliers : 0.00 % Allowed : 30.00 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -8.65 (0.56), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.59 (0.42), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.023 0.005 TYR B 465 Details of bonding type rmsd covalent geometry : bond 0.00992 ( 513) covalent geometry : angle 1.54213 ( 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.011 Fit side-chains REVERT: B 465 TYR cc_start: 0.8242 (p90) cc_final: 0.7727 (p90) REVERT: A 449 LEU cc_start: 0.8704 (pt) cc_final: 0.8504 (pt) REVERT: A 453 TYR cc_start: 0.5824 (p90) cc_final: 0.5543 (p90) REVERT: C 468 MET cc_start: 0.7834 (ttp) cc_final: 0.7455 (ttt) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0156 time to fit residues: 0.5266 Evaluate side-chains 25 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.011 ------------------------------------------------------------------------------- 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: 2.9990 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.161103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.118512 restraints weight = 745.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.123134 restraints weight = 486.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.126712 restraints weight = 374.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.129033 restraints weight = 316.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.130027 restraints weight = 278.829| |-----------------------------------------------------------------------------| r_work (final): 0.4361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6063 moved from start: 0.5664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 513 Z= 0.196 Angle : 0.891 5.551 696 Z= 0.475 Chirality : 0.042 0.143 81 Planarity : 0.004 0.012 90 Dihedral : 7.445 20.299 69 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 31.67 % Favored : 68.33 % Rotamer: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -7.41 (0.62), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.64 (0.47), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.022 0.004 TYR B 453 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 513) covalent geometry : angle 0.89070 ( 696) *********************** REFINEMENT MACRO_CYCLE 2 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.011 Fit side-chains revert: symmetry clash REVERT: A 451 ASN cc_start: 0.8099 (m-40) cc_final: 0.7817 (p0) REVERT: C 453 TYR cc_start: 0.5811 (p90) cc_final: 0.5344 (p90) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0121 time to fit residues: 0.4766 Evaluate side-chains 32 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.017 ------------------------------------------------------------------------------- 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: 4.9990 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 0.0040 chunk 3 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 overall best weight: 0.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 459 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5347 r_free = 0.5347 target = 0.332762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.5590 r_free = 0.5590 target = 0.266565 restraints weight = 962.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.5590 r_free = 0.5590 target = 0.266565 restraints weight = 1003.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5590 r_free = 0.5590 target = 0.266565 restraints weight = 1003.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.5590 r_free = 0.5590 target = 0.266565 restraints weight = 1003.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5590 r_free = 0.5590 target = 0.266565 restraints weight = 1003.624| |-----------------------------------------------------------------------------| r_work (final): 0.5014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6109 moved from start: 0.7111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 513 Z= 0.145 Angle : 0.755 4.665 696 Z= 0.398 Chirality : 0.038 0.118 81 Planarity : 0.003 0.012 90 Dihedral : 6.524 17.289 69 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 21.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.00 % Favored : 75.00 % Rotamer: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.49 (0.75), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.94 (0.57), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.002 TYR B 453 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 513) covalent geometry : angle 0.75483 ( 696) *********************** REFINEMENT MACRO_CYCLE 3 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.011 Fit side-chains revert: symmetry clash REVERT: A 463 ASN cc_start: 0.5946 (p0) cc_final: 0.5611 (p0) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0132 time to fit residues: 0.5131 Evaluate side-chains 31 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.011 ------------------------------------------------------------------------------- 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: 3.9990 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 0.0060 chunk 3 optimal weight: 0.4980 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 overall best weight: 0.4007 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 451 ASN A 459 GLN C 454 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.174749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.129046 restraints weight = 709.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.134382 restraints weight = 485.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.137672 restraints weight = 372.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.141537 restraints weight = 311.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.143255 restraints weight = 271.269| |-----------------------------------------------------------------------------| r_work (final): 0.4488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6035 moved from start: 0.7972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 513 Z= 0.153 Angle : 0.757 5.458 696 Z= 0.403 Chirality : 0.041 0.145 81 Planarity : 0.003 0.013 90 Dihedral : 6.274 15.665 69 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 35.00 % Favored : 65.00 % Rotamer: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.38 (0.77), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.86 (0.59), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.002 TYR B 453 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 513) covalent geometry : angle 0.75716 ( 696) *********************** REFINEMENT MACRO_CYCLE 4 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.011 Fit side-chains REVERT: B 449 LEU cc_start: 0.8417 (pt) cc_final: 0.8190 (pt) REVERT: B 451 ASN cc_start: 0.8132 (m-40) cc_final: 0.6301 (t0) REVERT: A 463 ASN cc_start: 0.6019 (p0) cc_final: 0.5709 (p0) REVERT: C 451 ASN cc_start: 0.7734 (m110) cc_final: 0.7444 (t0) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0124 time to fit residues: 0.4689 Evaluate side-chains 29 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.011 ------------------------------------------------------------------------------- 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: 4.9990 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 0.0070 chunk 3 optimal weight: 0.0060 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 0.0050 overall best weight: 0.0060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5021 r_free = 0.5021 target = 0.219686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.166324 restraints weight = 644.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.174900 restraints weight = 391.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.181909 restraints weight = 277.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.186149 restraints weight = 209.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4868 r_free = 0.4868 target = 0.190045 restraints weight = 171.989| |-----------------------------------------------------------------------------| r_work (final): 0.4863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5687 moved from start: 0.9076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 513 Z= 0.152 Angle : 0.753 4.581 696 Z= 0.404 Chirality : 0.043 0.148 81 Planarity : 0.003 0.010 90 Dihedral : 5.581 14.557 69 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.33 % Favored : 81.67 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.00 (0.76), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.57 (0.58), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.002 TYR B 453 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 513) covalent geometry : angle 0.75342 ( 696) *********************** REFINEMENT MACRO_CYCLE 5 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.012 Fit side-chains revert: symmetry clash REVERT: B 451 ASN cc_start: 0.8225 (m-40) cc_final: 0.7063 (t0) REVERT: A 463 ASN cc_start: 0.6093 (p0) cc_final: 0.5756 (p0) REVERT: C 451 ASN cc_start: 0.7768 (m110) cc_final: 0.7362 (t0) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0127 time to fit residues: 0.4527 Evaluate side-chains 25 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.011 ------------------------------------------------------------------------------- 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: 3.9990 chunk 1 optimal weight: 0.2980 chunk 2 optimal weight: 0.1980 chunk 3 optimal weight: 0.0060 chunk 4 optimal weight: 0.4980 chunk 5 optimal weight: 0.0270 overall best weight: 0.0770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 451 ASN A 459 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5080 r_free = 0.5080 target = 0.340109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4868 r_free = 0.4868 target = 0.211520 restraints weight = 1018.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.4874 r_free = 0.4874 target = 0.217148 restraints weight = 756.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4959 r_free = 0.4959 target = 0.223701 restraints weight = 624.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4968 r_free = 0.4968 target = 0.227569 restraints weight = 522.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.5009 r_free = 0.5009 target = 0.233460 restraints weight = 458.916| |-----------------------------------------------------------------------------| r_work (final): 0.4775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5707 moved from start: 0.9807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 513 Z= 0.145 Angle : 0.724 4.609 696 Z= 0.378 Chirality : 0.040 0.130 81 Planarity : 0.003 0.010 90 Dihedral : 5.008 12.183 69 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.52 (0.75), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.20 (0.57), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR B 453 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 513) covalent geometry : angle 0.72383 ( 696) *********************** REFINEMENT MACRO_CYCLE 6 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.012 Fit side-chains revert: symmetry clash REVERT: B 451 ASN cc_start: 0.8208 (m110) cc_final: 0.6950 (t0) REVERT: A 451 ASN cc_start: 0.7509 (p0) cc_final: 0.7302 (p0) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0139 time to fit residues: 0.4769 Evaluate side-chains 22 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.011 ------------------------------------------------------------------------------- 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: 3.9990 chunk 1 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 overall best weight: 0.5647 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 459 GLN A 459 GLN A 464 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4981 r_free = 0.4981 target = 0.326650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.182545 restraints weight = 1096.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.188233 restraints weight = 794.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4870 r_free = 0.4870 target = 0.196133 restraints weight = 645.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.199854 restraints weight = 509.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4897 r_free = 0.4897 target = 0.203592 restraints weight = 444.453| |-----------------------------------------------------------------------------| r_work (final): 0.4571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5921 moved from start: 0.9732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 513 Z= 0.184 Angle : 0.789 5.939 696 Z= 0.425 Chirality : 0.043 0.138 81 Planarity : 0.003 0.009 90 Dihedral : 6.188 17.307 69 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 31.67 % Favored : 68.33 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.72 (0.73), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.35 (0.56), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.002 TYR B 453 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 513) covalent geometry : angle 0.78892 ( 696) *********************** REFINEMENT MACRO_CYCLE 7 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.012 Fit side-chains REVERT: B 465 TYR cc_start: 0.7153 (p90) cc_final: 0.6932 (p90) REVERT: A 456 SER cc_start: 0.8574 (t) cc_final: 0.8359 (t) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0159 time to fit residues: 0.5568 Evaluate side-chains 29 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.032 ------------------------------------------------------------------------------- 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: 3.9990 chunk 1 optimal weight: 0.3980 chunk 2 optimal weight: 0.0870 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 overall best weight: 0.2610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5109 r_free = 0.5109 target = 0.238913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.170094 restraints weight = 774.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.175839 restraints weight = 552.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.181293 restraints weight = 442.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.185173 restraints weight = 374.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.185174 restraints weight = 330.019| |-----------------------------------------------------------------------------| r_work (final): 0.4751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6199 moved from start: 1.0347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 513 Z= 0.161 Angle : 0.780 4.754 696 Z= 0.410 Chirality : 0.043 0.162 81 Planarity : 0.003 0.012 90 Dihedral : 5.502 12.507 69 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.67 % Favored : 78.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.52 (0.75), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.20 (0.57), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.002 TYR B 453 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 513) covalent geometry : angle 0.77953 ( 696) *********************** REFINEMENT MACRO_CYCLE 8 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.012 Fit side-chains REVERT: B 467 THR cc_start: 0.9213 (t) cc_final: 0.8598 (m) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0119 time to fit residues: 0.4000 Evaluate side-chains 28 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.011 ------------------------------------------------------------------------------- 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: 3.9990 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 overall best weight: 0.8647 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4941 r_free = 0.4941 target = 0.211338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.153825 restraints weight = 746.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.158141 restraints weight = 538.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.160468 restraints weight = 439.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.164089 restraints weight = 394.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.164169 restraints weight = 347.177| |-----------------------------------------------------------------------------| r_work (final): 0.4461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6062 moved from start: 1.0237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 513 Z= 0.223 Angle : 0.837 5.371 696 Z= 0.451 Chirality : 0.045 0.122 81 Planarity : 0.003 0.008 90 Dihedral : 6.831 18.789 69 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 36.67 % Favored : 63.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.65 (0.78), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.30 (0.60), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYR B 465 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 513) covalent geometry : angle 0.83707 ( 696) *********************** REFINEMENT MACRO_CYCLE 9 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.013 Fit side-chains REVERT: B 465 TYR cc_start: 0.7073 (p90) cc_final: 0.6796 (p90) REVERT: B 466 LEU cc_start: 0.8033 (pp) cc_final: 0.7728 (pp) REVERT: B 467 THR cc_start: 0.9027 (t) cc_final: 0.8175 (m) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0123 time to fit residues: 0.4584 Evaluate side-chains 29 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.013 ------------------------------------------------------------------------------- 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: 5.9990 chunk 2 optimal weight: 0.0030 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 overall best weight: 0.3663 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4982 r_free = 0.4982 target = 0.213647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.154511 restraints weight = 747.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.158664 restraints weight = 568.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.161848 restraints weight = 475.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.164788 restraints weight = 418.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.165990 restraints weight = 376.460| |-----------------------------------------------------------------------------| r_work (final): 0.4530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6002 moved from start: 1.0687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 513 Z= 0.179 Angle : 0.802 4.920 696 Z= 0.431 Chirality : 0.044 0.157 81 Planarity : 0.003 0.012 90 Dihedral : 6.097 14.407 69 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.00 % Favored : 75.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.55 (0.79), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.22 (0.61), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR A 453 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 513) covalent geometry : angle 0.80201 ( 696) ********************** REFINEMENT MACRO_CYCLE 10 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.028 Fit side-chains REVERT: B 451 ASN cc_start: 0.8102 (p0) cc_final: 0.7367 (t0) REVERT: B 466 LEU cc_start: 0.7981 (pp) cc_final: 0.7698 (pp) REVERT: B 467 THR cc_start: 0.9054 (t) cc_final: 0.8033 (m) REVERT: A 456 SER cc_start: 0.8348 (t) cc_final: 0.8068 (t) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0251 time to fit residues: 0.8542 Evaluate side-chains 26 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.027 ------------------------------------------------------------------------------- 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: 3.9990 chunk 2 optimal weight: 0.0020 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.0980 chunk 5 optimal weight: 0.6980 overall best weight: 0.2660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5146 r_free = 0.5146 target = 0.235509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.168997 restraints weight = 681.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.173744 restraints weight = 504.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4857 r_free = 0.4857 target = 0.175983 restraints weight = 416.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4875 r_free = 0.4875 target = 0.179968 restraints weight = 376.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.182092 restraints weight = 336.027| |-----------------------------------------------------------------------------| r_work (final): 0.4659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5895 moved from start: 1.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 513 Z= 0.169 Angle : 0.794 4.829 696 Z= 0.422 Chirality : 0.045 0.170 81 Planarity : 0.003 0.015 90 Dihedral : 5.469 14.890 69 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.67 % Favored : 73.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.46 (0.79), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.16 (0.60), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.002 TYR A 453 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 513) covalent geometry : angle 0.79358 ( 696) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 269.99 seconds wall clock time: 5 minutes 23.44 seconds (323.44 seconds total)