Starting phenix.real_space_refine on Mon Feb 10 19:25:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7da4_30622/02_2025/7da4_30622.cif Found real_map, /net/cci-nas-00/data/ceres_data/7da4_30622/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7da4_30622/02_2025/7da4_30622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7da4_30622/02_2025/7da4_30622.map" model { file = "/net/cci-nas-00/data/ceres_data/7da4_30622/02_2025/7da4_30622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7da4_30622/02_2025/7da4_30622.cif" } resolution = 4.24 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= 0.001 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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 507 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" 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: C, B Time building chain proxies: 0.70, per 1000 atoms: 1.38 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: 0.22 Conformation dependent library (CDL) restraints added in 596.9 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: 3.41 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: 0.25 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 'A' selection = chain 'C' selection = chain 'B' } 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: 1.000 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: 0.010 Extract box with map and model: 0.020 Check model and map are aligned: 0.000 Set scattering table: 0.030 Process input model: 7.140 Find NCS groups from input model: 0.010 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:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.570 ------------------------------------------------------------------------------- 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 (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: -8.65 (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 *********************** 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 : 0.047 Fit side-chains REVERT: B 465 TYR cc_start: 0.8242 (p90) cc_final: 0.7727 (p90) REVERT: A 453 TYR cc_start: 0.5824 (p90) cc_final: 0.5543 (p90) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0581 time to fit residues: 1.9325 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 : 0.045 ------------------------------------------------------------------------------- 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: 0.7980 chunk 2 optimal weight: 0.0970 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 0.0040 chunk 5 optimal weight: 0.9990 overall best weight: 0.2997 ------------------------------------------------------------------------------- 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 = 0.4728 r_free = 0.4728 target = 0.162315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.118431 restraints weight = 695.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.122669 restraints weight = 465.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.126021 restraints weight = 367.211| |-----------------------------------------------------------------------------| r_work (final): 0.4352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6026 moved from start: 0.5709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 513 Z= 0.178 Angle : 0.902 5.280 696 Z= 0.478 Chirality : 0.042 0.144 81 Planarity : 0.004 0.013 90 Dihedral : 7.070 19.179 69 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 22.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.00 % Favored : 75.00 % 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: -7.16 (0.66), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.45 (0.51), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.021 0.003 TYR B 453 *********************** 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 33 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.061 Fit side-chains revert: symmetry clash REVERT: A 451 ASN cc_start: 0.8142 (m-40) cc_final: 0.7852 (p0) REVERT: C 453 TYR cc_start: 0.5671 (p90) cc_final: 0.5164 (p90) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0621 time to fit residues: 2.3098 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 : 0.063 ------------------------------------------------------------------------------- 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: 0.9990 chunk 2 optimal weight: 0.0170 chunk 3 optimal weight: 0.1980 chunk 4 optimal weight: 0.0020 chunk 5 optimal weight: 0.9980 overall best weight: 0.0723 ------------------------------------------------------------------------------- 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 = 0.5475 r_free = 0.5475 target = 0.382315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.5881 r_free = 0.5881 target = 0.302557 restraints weight = 1103.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.5881 r_free = 0.5881 target = 0.302557 restraints weight = 1073.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5881 r_free = 0.5881 target = 0.302557 restraints weight = 1073.445| |-----------------------------------------------------------------------------| r_work (final): 0.5021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5869 moved from start: 0.8087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 513 Z= 0.129 Angle : 0.698 3.793 696 Z= 0.380 Chirality : 0.039 0.114 81 Planarity : 0.003 0.012 90 Dihedral : 5.872 16.209 69 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % 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 (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: -6.25 (0.78), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.76 (0.60), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.002 TYR B 453 *********************** 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 29 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.073 Fit side-chains revert: symmetry clash REVERT: A 451 ASN cc_start: 0.6784 (m-40) cc_final: 0.6507 (p0) REVERT: A 453 TYR cc_start: 0.5939 (p90) cc_final: 0.5700 (p90) REVERT: A 456 SER cc_start: 0.8352 (t) cc_final: 0.8038 (t) REVERT: A 463 ASN cc_start: 0.5444 (p0) cc_final: 0.5110 (p0) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0613 time to fit residues: 2.0085 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 : 0.074 ------------------------------------------------------------------------------- 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: 0.8980 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 0.0670 chunk 5 optimal weight: 0.5980 overall best weight: 0.4877 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 GLN C 459 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5150 r_free = 0.5150 target = 0.189271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.160249 restraints weight = 803.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.160249 restraints weight = 812.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.160249 restraints weight = 812.089| |-----------------------------------------------------------------------------| r_work (final): 0.4827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6196 moved from start: 0.8014 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= 0.140 Angle : 0.731 6.541 696 Z= 0.370 Chirality : 0.036 0.114 81 Planarity : 0.003 0.010 90 Dihedral : 6.044 17.050 69 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 30.00 % Favored : 70.00 % Rotamer: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -6.31 (0.79), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.81 (0.60), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.020 0.002 TYR B 453 *********************** 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 35 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.062 Fit side-chains REVERT: B 458 VAL cc_start: 0.8914 (p) cc_final: 0.8690 (m) REVERT: A 449 LEU cc_start: 0.8089 (pt) cc_final: 0.7874 (pt) REVERT: A 456 SER cc_start: 0.8337 (t) cc_final: 0.7941 (t) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0613 time to fit residues: 2.3942 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 : 0.063 ------------------------------------------------------------------------------- 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: 0.9980 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 459 GLN C 454 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.297815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4926 r_free = 0.4926 target = 0.176375 restraints weight = 971.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4950 r_free = 0.4950 target = 0.182113 restraints weight = 643.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4973 r_free = 0.4973 target = 0.185813 restraints weight = 505.103| |-----------------------------------------------------------------------------| r_work (final): 0.4449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6221 moved from start: 0.8608 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= 0.163 Angle : 0.743 5.035 696 Z= 0.392 Chirality : 0.039 0.132 81 Planarity : 0.003 0.019 90 Dihedral : 6.441 16.090 69 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 28.33 % Favored : 71.67 % 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: -6.16 (0.72), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.69 (0.55), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.002 TYR B 453 *********************** 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 34 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.055 Fit side-chains REVERT: B 467 THR cc_start: 0.9074 (t) cc_final: 0.7951 (m) REVERT: A 456 SER cc_start: 0.8551 (t) cc_final: 0.8320 (t) REVERT: C 468 MET cc_start: 0.8418 (ttt) cc_final: 0.8200 (ttm) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0547 time to fit residues: 2.0951 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 : 0.062 ------------------------------------------------------------------------------- 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: 0.3980 chunk 2 optimal weight: 0.0050 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 overall best weight: 0.4337 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 459 GLN ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5295 r_free = 0.5295 target = 0.334686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.5563 r_free = 0.5563 target = 0.265270 restraints weight = 999.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.5563 r_free = 0.5563 target = 0.265268 restraints weight = 1053.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5563 r_free = 0.5563 target = 0.265268 restraints weight = 1053.687| |-----------------------------------------------------------------------------| r_work (final): 0.4985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6106 moved from start: 0.9123 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= 0.162 Angle : 0.777 5.371 696 Z= 0.418 Chirality : 0.042 0.147 81 Planarity : 0.003 0.009 90 Dihedral : 6.329 18.094 69 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 17.17 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 (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: -6.27 (0.70), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.77 (0.54), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.002 TYR B 453 *********************** 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 35 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.065 Fit side-chains REVERT: B 467 THR cc_start: 0.9062 (t) cc_final: 0.8555 (m) REVERT: A 456 SER cc_start: 0.8497 (t) cc_final: 0.8127 (t) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0550 time to fit residues: 2.1790 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 : 0.059 ------------------------------------------------------------------------------- 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: 0.0970 chunk 2 optimal weight: 0.0970 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.2973 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 ASN 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 = 0.5326 r_free = 0.5326 target = 0.332592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.5551 r_free = 0.5551 target = 0.256229 restraints weight = 1018.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.5552 r_free = 0.5552 target = 0.256501 restraints weight = 995.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.5552 r_free = 0.5552 target = 0.256550 restraints weight = 980.040| |-----------------------------------------------------------------------------| r_work (final): 0.5173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6136 moved from start: 0.9967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 513 Z= 0.163 Angle : 0.794 4.735 696 Z= 0.418 Chirality : 0.043 0.120 81 Planarity : 0.003 0.009 90 Dihedral : 5.997 13.524 69 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.33 % Favored : 76.67 % Rotamer: Outliers : 1.67 % Allowed : 3.33 % 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: -6.16 (0.71), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.69 (0.54), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.002 TYR B 453 *********************** 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: 1 poor density : 30 time to evaluate : 0.062 Fit side-chains REVERT: B 450 VAL cc_start: 0.8458 (m) cc_final: 0.8197 (m) REVERT: B 467 THR cc_start: 0.9153 (t) cc_final: 0.8577 (m) outliers start: 1 outliers final: 0 residues processed: 31 average time/residue: 0.0616 time to fit residues: 2.1718 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 : 0.059 ------------------------------------------------------------------------------- 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: 0.9980 chunk 2 optimal weight: 0.0370 chunk 3 optimal weight: 0.4980 chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 0.2980 overall best weight: 0.2777 ------------------------------------------------------------------------------- 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 = 0.4964 r_free = 0.4964 target = 0.302750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4922 r_free = 0.4922 target = 0.196281 restraints weight = 953.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4951 r_free = 0.4951 target = 0.201220 restraints weight = 743.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4954 r_free = 0.4954 target = 0.201799 restraints weight = 623.447| |-----------------------------------------------------------------------------| r_work (final): 0.4555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5893 moved from start: 1.0312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 513 Z= 0.153 Angle : 0.760 5.337 696 Z= 0.391 Chirality : 0.043 0.125 81 Planarity : 0.002 0.008 90 Dihedral : 5.854 15.193 69 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.33 % Favored : 76.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.02 (0.68), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.58 (0.52), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYR B 453 *********************** 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 30 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.057 Fit side-chains REVERT: B 451 ASN cc_start: 0.7980 (m110) cc_final: 0.7370 (t0) REVERT: B 465 TYR cc_start: 0.6797 (p90) cc_final: 0.6523 (p90) REVERT: B 467 THR cc_start: 0.9051 (t) cc_final: 0.8310 (m) REVERT: C 456 SER cc_start: 0.7496 (t) cc_final: 0.7126 (t) REVERT: C 468 MET cc_start: 0.8065 (ttm) cc_final: 0.7814 (ttm) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0571 time to fit residues: 1.9543 Evaluate side-chains 27 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.053 ------------------------------------------------------------------------------- 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: 0.0470 chunk 2 optimal weight: 0.1980 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 overall best weight: 0.3143 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 459 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5363 r_free = 0.5363 target = 0.341472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.5583 r_free = 0.5583 target = 0.264541 restraints weight = 1063.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.5583 r_free = 0.5583 target = 0.264541 restraints weight = 1017.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5583 r_free = 0.5583 target = 0.264541 restraints weight = 1017.254| |-----------------------------------------------------------------------------| r_work (final): 0.4916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6116 moved from start: 1.0440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 513 Z= 0.152 Angle : 0.753 4.671 696 Z= 0.389 Chirality : 0.042 0.109 81 Planarity : 0.002 0.008 90 Dihedral : 5.622 13.630 69 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.33 % Favored : 76.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.84 (0.71), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.45 (0.54), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.002 TYR A 453 *********************** 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 29 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.064 Fit side-chains REVERT: B 467 THR cc_start: 0.9213 (t) cc_final: 0.8475 (m) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0550 time to fit residues: 1.8189 Evaluate side-chains 27 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 0.0370 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 overall best weight: 0.5443 ------------------------------------------------------------------------------- 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 = 0.4976 r_free = 0.4976 target = 0.183483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.131326 restraints weight = 777.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.132890 restraints weight = 620.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.134940 restraints weight = 551.162| |-----------------------------------------------------------------------------| r_work (final): 0.4419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6187 moved from start: 1.0505 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= 0.174 Angle : 0.779 5.079 696 Z= 0.405 Chirality : 0.044 0.119 81 Planarity : 0.003 0.009 90 Dihedral : 6.376 16.657 69 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 28.33 % Favored : 71.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.75 (0.73), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.38 (0.56), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.022 0.003 TYR A 453 ********************** 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 28 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.056 Fit side-chains REVERT: B 467 THR cc_start: 0.9230 (t) cc_final: 0.8261 (m) REVERT: C 456 SER cc_start: 0.7657 (t) cc_final: 0.7456 (t) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0573 time to fit residues: 1.8328 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 : 0.063 ------------------------------------------------------------------------------- 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: 2.9990 chunk 2 optimal weight: 0.3980 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 0.0070 chunk 5 optimal weight: 0.0030 overall best weight: 0.1360 ------------------------------------------------------------------------------- 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 = 0.5406 r_free = 0.5406 target = 0.349330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.5636 r_free = 0.5636 target = 0.275783 restraints weight = 1028.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.5636 r_free = 0.5636 target = 0.275783 restraints weight = 990.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5636 r_free = 0.5636 target = 0.275783 restraints weight = 990.364| |-----------------------------------------------------------------------------| r_work (final): 0.5253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5993 moved from start: 1.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 513 Z= 0.145 Angle : 0.733 4.838 696 Z= 0.378 Chirality : 0.041 0.111 81 Planarity : 0.002 0.008 90 Dihedral : 5.174 12.326 69 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % 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: -5.69 (0.72), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.33 (0.55), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.002 TYR A 453 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 632.23 seconds wall clock time: 13 minutes 6.94 seconds (786.94 seconds total)