Starting phenix.real_space_refine on Wed Mar 5 14:15:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7da4_30622/03_2025/7da4_30622.cif Found real_map, /net/cci-nas-00/data/ceres_data/7da4_30622/03_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_30622/03_2025/7da4_30622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7da4_30622/03_2025/7da4_30622.map" model { file = "/net/cci-nas-00/data/ceres_data/7da4_30622/03_2025/7da4_30622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7da4_30622/03_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-5624/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: 0.86, per 1000 atoms: 1.70 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: 0.14 Conformation dependent library (CDL) restraints added in 75.5 milliseconds 120 Ramachandran restraints generated. 60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 120 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 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: 0.18 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: 0.01 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: 1.200 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: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.840 Find NCS groups from input model: 0.020 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:3.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.940 ------------------------------------------------------------------------------- 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 : 0.046 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: 0.0810 time to fit residues: 2.6197 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 : 0.046 ------------------------------------------------------------------------------- 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: 0.8980 chunk 3 optimal weight: 0.0670 chunk 4 optimal weight: 0.0040 chunk 5 optimal weight: 0.6980 overall best weight: 0.2563 ------------------------------------------------------------------------------- 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 = 0.5089 r_free = 0.5089 target = 0.184742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.152233 restraints weight = 805.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.152232 restraints weight = 809.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.152231 restraints weight = 809.255| |-----------------------------------------------------------------------------| r_work (final): 0.4411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6016 moved from start: 0.5718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 513 Z= 0.178 Angle : 0.892 5.185 696 Z= 0.475 Chirality : 0.042 0.149 81 Planarity : 0.003 0.011 90 Dihedral : 7.141 19.377 69 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 23.23 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: -7.20 (0.67), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.48 (0.51), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.021 0.004 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: B 449 LEU cc_start: 0.8220 (pt) cc_final: 0.8003 (pt) REVERT: B 465 TYR cc_start: 0.7929 (p90) cc_final: 0.7670 (p90) REVERT: A 451 ASN cc_start: 0.7979 (m-40) cc_final: 0.7731 (p0) REVERT: C 453 TYR cc_start: 0.5634 (p90) cc_final: 0.5219 (p90) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0610 time to fit residues: 2.2717 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 : 0.122 ------------------------------------------------------------------------------- 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: 0.2980 chunk 3 optimal weight: 0.0470 chunk 4 optimal weight: 0.1980 chunk 5 optimal weight: 0.0970 overall best weight: 0.1140 ------------------------------------------------------------------------------- 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 = 0.5443 r_free = 0.5443 target = 0.378201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.5843 r_free = 0.5843 target = 0.297819 restraints weight = 1101.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.5843 r_free = 0.5843 target = 0.297818 restraints weight = 1083.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5843 r_free = 0.5843 target = 0.297818 restraints weight = 1083.522| |-----------------------------------------------------------------------------| r_work (final): 0.4969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5929 moved from start: 0.7946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.012 513 Z= 0.133 Angle : 0.692 3.652 696 Z= 0.373 Chirality : 0.038 0.112 81 Planarity : 0.003 0.012 90 Dihedral : 5.979 16.088 69 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.33 % Favored : 81.67 % 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: -6.31 (0.78), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.80 (0.59), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 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 31 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.054 Fit side-chains revert: symmetry clash REVERT: A 451 ASN cc_start: 0.6715 (m-40) cc_final: 0.6486 (p0) REVERT: A 453 TYR cc_start: 0.5902 (p90) cc_final: 0.5650 (p90) REVERT: A 456 SER cc_start: 0.8322 (t) cc_final: 0.8034 (t) REVERT: A 463 ASN cc_start: 0.5399 (p0) cc_final: 0.5033 (p0) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0590 time to fit residues: 2.0532 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 : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 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: A 459 GLN C 454 ASN C 459 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.169875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.126020 restraints weight = 727.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.129496 restraints weight = 529.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.132495 restraints weight = 427.978| |-----------------------------------------------------------------------------| r_work (final): 0.4428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6047 moved from start: 0.8052 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= 0.155 Angle : 0.736 6.311 696 Z= 0.375 Chirality : 0.036 0.116 81 Planarity : 0.003 0.010 90 Dihedral : 6.198 16.606 69 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 21.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 35.00 % Favored : 65.00 % Rotamer: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.41 (0.78), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.88 (0.59), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 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 34 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.063 Fit side-chains REVERT: B 465 TYR cc_start: 0.7776 (p90) cc_final: 0.7200 (p90) REVERT: A 449 LEU cc_start: 0.8575 (pt) cc_final: 0.8366 (pt) REVERT: A 451 ASN cc_start: 0.7895 (m-40) cc_final: 0.7663 (p0) REVERT: A 463 ASN cc_start: 0.6029 (p0) cc_final: 0.5692 (p0) REVERT: C 466 LEU cc_start: 0.7455 (pp) cc_final: 0.7168 (pp) REVERT: C 467 THR cc_start: 0.9387 (t) cc_final: 0.9071 (m) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0582 time to fit residues: 2.2262 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 : 0.060 ------------------------------------------------------------------------------- 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: 0.0980 chunk 2 optimal weight: 0.4980 chunk 3 optimal weight: 0.4980 chunk 4 optimal weight: 0.0870 chunk 5 optimal weight: 0.0770 overall best weight: 0.0873 ------------------------------------------------------------------------------- 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 = 0.5038 r_free = 0.5038 target = 0.202380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.156244 restraints weight = 639.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4789 r_free = 0.4789 target = 0.163049 restraints weight = 380.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.168146 restraints weight = 273.890| |-----------------------------------------------------------------------------| r_work (final): 0.4722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5852 moved from start: 0.8682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 513 Z= 0.123 Angle : 0.694 4.782 696 Z= 0.360 Chirality : 0.039 0.115 81 Planarity : 0.003 0.010 90 Dihedral : 5.567 14.725 69 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.67 % Favored : 78.33 % 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: -6.04 (0.75), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.60 (0.57), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.001 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 32 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.056 Fit side-chains REVERT: B 458 VAL cc_start: 0.8600 (p) cc_final: 0.8290 (m) REVERT: A 451 ASN cc_start: 0.8035 (m-40) cc_final: 0.7654 (p0) REVERT: C 466 LEU cc_start: 0.7443 (pp) cc_final: 0.7204 (pp) REVERT: C 467 THR cc_start: 0.9381 (t) cc_final: 0.9157 (m) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0584 time to fit residues: 2.1000 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 : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 4 optimal weight: 0.0870 chunk 5 optimal weight: 0.0670 overall best weight: 0.1840 ------------------------------------------------------------------------------- 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 = 0.5415 r_free = 0.5415 target = 0.378093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.5811 r_free = 0.5811 target = 0.294645 restraints weight = 1124.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.5811 r_free = 0.5811 target = 0.294645 restraints weight = 1060.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5811 r_free = 0.5811 target = 0.294645 restraints weight = 1060.634| |-----------------------------------------------------------------------------| r_work (final): 0.4840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5697 moved from start: 0.9021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 513 Z= 0.128 Angle : 0.694 4.727 696 Z= 0.361 Chirality : 0.037 0.113 81 Planarity : 0.002 0.009 90 Dihedral : 5.152 13.456 69 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 10.10 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: -5.76 (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 0.016 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 33 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.125 Fit side-chains REVERT: B 465 TYR cc_start: 0.7611 (p90) cc_final: 0.7104 (p90) REVERT: A 451 ASN cc_start: 0.7987 (m-40) cc_final: 0.7716 (p0) REVERT: C 466 LEU cc_start: 0.7182 (pp) cc_final: 0.6786 (pp) REVERT: C 467 THR cc_start: 0.9330 (t) cc_final: 0.9039 (m) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0657 time to fit residues: 2.4888 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 : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 overall best weight: 0.6313 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 459 GLN A 469 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4951 r_free = 0.4951 target = 0.172369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.116571 restraints weight = 778.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.119486 restraints weight = 619.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.121414 restraints weight = 527.265| |-----------------------------------------------------------------------------| r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6247 moved from start: 0.8980 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= 0.163 Angle : 0.717 5.367 696 Z= 0.375 Chirality : 0.038 0.120 81 Planarity : 0.003 0.009 90 Dihedral : 6.360 15.108 69 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 31.67 % Favored : 68.33 % 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 (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: -5.61 (0.74), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.27 (0.56), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 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 35 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.064 Fit side-chains revert: symmetry clash REVERT: B 451 ASN cc_start: 0.8165 (m110) cc_final: 0.7366 (t0) REVERT: B 466 LEU cc_start: 0.8005 (pp) cc_final: 0.7791 (pp) REVERT: B 467 THR cc_start: 0.8967 (t) cc_final: 0.7949 (m) REVERT: A 451 ASN cc_start: 0.8277 (m-40) cc_final: 0.8007 (p0) REVERT: A 456 SER cc_start: 0.8584 (t) cc_final: 0.8375 (t) REVERT: C 467 THR cc_start: 0.9358 (t) cc_final: 0.9146 (m) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0559 time to fit residues: 2.2029 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 : 0.060 ------------------------------------------------------------------------------- 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: 1.9990 chunk 2 optimal weight: 0.0270 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.5077 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5306 r_free = 0.5306 target = 0.327204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5497 r_free = 0.5497 target = 0.251778 restraints weight = 1003.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.5497 r_free = 0.5497 target = 0.251778 restraints weight = 1012.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5497 r_free = 0.5497 target = 0.251778 restraints weight = 1012.007| |-----------------------------------------------------------------------------| r_work (final): 0.4888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6234 moved from start: 0.9429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 513 Z= 0.157 Angle : 0.729 5.074 696 Z= 0.384 Chirality : 0.037 0.116 81 Planarity : 0.003 0.008 90 Dihedral : 6.074 17.689 69 Min Nonbonded Distance : 2.591 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 (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: -5.67 (0.72), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.32 (0.55), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.002 TYR B 465 *********************** 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 32 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.060 Fit side-chains revert: symmetry clash REVERT: B 451 ASN cc_start: 0.7297 (m110) cc_final: 0.6853 (t0) REVERT: B 467 THR cc_start: 0.9197 (t) cc_final: 0.8648 (m) REVERT: A 451 ASN cc_start: 0.7377 (m-40) cc_final: 0.6928 (p0) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0589 time to fit residues: 2.1240 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 : 0.060 ------------------------------------------------------------------------------- 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: 0.0970 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 0.4980 chunk 5 optimal weight: 0.0060 overall best weight: 0.2003 ------------------------------------------------------------------------------- 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 = 0.4935 r_free = 0.4935 target = 0.292323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4965 r_free = 0.4965 target = 0.192489 restraints weight = 976.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.5038 r_free = 0.5038 target = 0.200038 restraints weight = 663.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.5069 r_free = 0.5069 target = 0.205310 restraints weight = 492.336| |-----------------------------------------------------------------------------| r_work (final): 0.4890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6225 moved from start: 1.0005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 513 Z= 0.144 Angle : 0.736 5.046 696 Z= 0.379 Chirality : 0.038 0.113 81 Planarity : 0.002 0.009 90 Dihedral : 5.128 12.858 69 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 13.13 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: -5.85 (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 0.011 0.002 TYR B 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 30 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.056 Fit side-chains REVERT: B 467 THR cc_start: 0.9223 (t) cc_final: 0.8825 (m) REVERT: A 451 ASN cc_start: 0.7185 (m-40) cc_final: 0.6847 (p0) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0584 time to fit residues: 1.9746 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 : 0.055 ------------------------------------------------------------------------------- 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: 0.2980 chunk 2 optimal weight: 0.4980 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 0.0670 overall best weight: 0.2877 ------------------------------------------------------------------------------- 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 = 0.5322 r_free = 0.5322 target = 0.333017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.5556 r_free = 0.5556 target = 0.263286 restraints weight = 1030.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.5559 r_free = 0.5559 target = 0.263762 restraints weight = 974.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5559 r_free = 0.5559 target = 0.263762 restraints weight = 939.354| |-----------------------------------------------------------------------------| r_work (final): 0.4989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6020 moved from start: 1.0401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 513 Z= 0.141 Angle : 0.716 4.812 696 Z= 0.369 Chirality : 0.037 0.115 81 Planarity : 0.002 0.008 90 Dihedral : 5.173 14.058 69 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 11.11 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: -5.86 (0.70), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.46 (0.54), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.002 TYR B 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 : 0.059 Fit side-chains REVERT: B 467 THR cc_start: 0.9206 (t) cc_final: 0.8548 (m) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0641 time to fit residues: 2.0117 Evaluate side-chains 24 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.060 ------------------------------------------------------------------------------- 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: 0.0870 chunk 2 optimal weight: 0.0000 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 0.0270 chunk 5 optimal weight: 0.9980 overall best weight: 0.0380 ------------------------------------------------------------------------------- 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 = 0.4943 r_free = 0.4943 target = 0.311072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4949 r_free = 0.4949 target = 0.204287 restraints weight = 995.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.5013 r_free = 0.5013 target = 0.211731 restraints weight = 692.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.5034 r_free = 0.5034 target = 0.217485 restraints weight = 534.055| |-----------------------------------------------------------------------------| r_work (final): 0.4769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6104 moved from start: 1.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 513 Z= 0.151 Angle : 0.735 5.043 696 Z= 0.388 Chirality : 0.041 0.141 81 Planarity : 0.003 0.013 90 Dihedral : 4.581 12.133 69 Min Nonbonded Distance : 2.478 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: -5.70 (0.75), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.34 (0.57), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.002 TYR B 453 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 636.98 seconds wall clock time: 12 minutes 45.89 seconds (765.89 seconds total)