Starting phenix.real_space_refine on Mon Sep 23 11:31:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7da4_30622/09_2024/7da4_30622.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7da4_30622/09_2024/7da4_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7da4_30622/09_2024/7da4_30622.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7da4_30622/09_2024/7da4_30622.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7da4_30622/09_2024/7da4_30622.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7da4_30622/09_2024/7da4_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-5461/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: 0.65, per 1000 atoms: 1.28 Number of scatterers: 507 At special positions: 0 Unit cell: (42.4, 38.16, 29.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 102 8.00 N 84 7.00 C 315 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.13 Conformation dependent library (CDL) restraints added in 61.1 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: 0.14 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: 0.17 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 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.020 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.330 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.640 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.065 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: 0.0758 time to fit residues: 2.5061 Evaluate side-chains 25 residues out of total 60 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.057 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6310 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 fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.065 Fit side-chains revert: symmetry clash REVERT: A 451 ASN cc_start: 0.7636 (m-40) cc_final: 0.7363 (p0) REVERT: C 453 TYR cc_start: 0.5573 (p90) cc_final: 0.5229 (p90) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0575 time to fit residues: 2.1410 Evaluate side-chains 32 residues out of total 60 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.065 ------------------------------------------------------------------------------- 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: 0.0980 chunk 2 optimal weight: 0.2980 chunk 3 optimal weight: 0.0270 chunk 4 optimal weight: 0.0030 chunk 5 optimal weight: 0.6980 overall best weight: 0.0427 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6031 moved from start: 0.8010 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= 0.131 Angle : 0.707 3.783 696 Z= 0.382 Chirality : 0.039 0.111 81 Planarity : 0.003 0.012 90 Dihedral : 5.817 15.972 69 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 16.16 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: -6.20 (0.78), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.72 (0.59), 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 fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.066 Fit side-chains revert: symmetry clash REVERT: B 463 ASN cc_start: 0.5624 (p0) cc_final: 0.5422 (p0) REVERT: B 468 MET cc_start: 0.7821 (ttt) cc_final: 0.6935 (ttm) REVERT: A 451 ASN cc_start: 0.7609 (m-40) cc_final: 0.7079 (p0) REVERT: A 453 TYR cc_start: 0.5931 (p90) cc_final: 0.5729 (p90) REVERT: A 456 SER cc_start: 0.8589 (t) cc_final: 0.8270 (t) REVERT: A 463 ASN cc_start: 0.6070 (p0) cc_final: 0.5669 (p0) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0623 time to fit residues: 2.0324 Evaluate side-chains 26 residues out of total 60 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.061 ------------------------------------------------------------------------------- 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: 0.7980 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 0.0570 chunk 5 optimal weight: 0.6980 overall best weight: 0.5177 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6297 moved from start: 0.7894 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= 0.148 Angle : 0.736 6.755 696 Z= 0.376 Chirality : 0.036 0.115 81 Planarity : 0.003 0.010 90 Dihedral : 6.133 17.212 69 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 18.18 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: -6.33 (0.78), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.82 (0.60), 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 35 residues out of total 60 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.062 Fit side-chains REVERT: B 463 ASN cc_start: 0.6069 (p0) cc_final: 0.5678 (p0) REVERT: A 449 LEU cc_start: 0.8503 (pt) cc_final: 0.8291 (pt) REVERT: A 451 ASN cc_start: 0.7717 (m-40) cc_final: 0.7332 (p0) REVERT: A 463 ASN cc_start: 0.5714 (p0) cc_final: 0.5398 (p0) REVERT: C 467 THR cc_start: 0.9372 (t) cc_final: 0.9062 (m) REVERT: C 468 MET cc_start: 0.8312 (ttt) cc_final: 0.8102 (ttm) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0596 time to fit residues: 2.3376 Evaluate side-chains 32 residues out of total 60 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.4980 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 0.0770 overall best weight: 0.4243 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6309 moved from start: 0.8412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 513 Z= 0.130 Angle : 0.683 4.770 696 Z= 0.348 Chirality : 0.035 0.116 81 Planarity : 0.003 0.011 90 Dihedral : 5.756 14.811 69 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.67 % Favored : 73.33 % 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: -6.07 (0.75), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.62 (0.57), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 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 fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.066 Fit side-chains REVERT: B 463 ASN cc_start: 0.6214 (p0) cc_final: 0.5913 (p0) REVERT: B 467 THR cc_start: 0.9144 (t) cc_final: 0.8041 (m) REVERT: A 451 ASN cc_start: 0.7829 (m-40) cc_final: 0.7432 (p0) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0632 time to fit residues: 2.4146 Evaluate side-chains 31 residues out of total 60 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.057 ------------------------------------------------------------------------------- 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: 0.2980 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 0.0030 overall best weight: 0.3997 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6249 moved from start: 0.8751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 513 Z= 0.131 Angle : 0.711 4.901 696 Z= 0.366 Chirality : 0.035 0.115 81 Planarity : 0.002 0.009 90 Dihedral : 5.864 14.182 69 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.33 % Favored : 76.67 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -6.23 (0.69), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.74 (0.52), 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 34 residues out of total 60 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.056 Fit side-chains REVERT: B 463 ASN cc_start: 0.6095 (p0) cc_final: 0.5805 (p0) REVERT: B 467 THR cc_start: 0.9144 (t) cc_final: 0.8484 (m) REVERT: A 451 ASN cc_start: 0.7888 (m-40) cc_final: 0.7381 (p0) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0614 time to fit residues: 2.3314 Evaluate side-chains 29 residues out of total 60 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 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: 4.9990 chunk 1 optimal weight: 0.0670 chunk 2 optimal weight: 0.2980 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 overall best weight: 0.3543 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6241 moved from start: 0.9384 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= 0.133 Angle : 0.709 5.118 696 Z= 0.363 Chirality : 0.036 0.112 81 Planarity : 0.002 0.006 90 Dihedral : 5.668 16.612 69 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.67 % Favored : 78.33 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -6.14 (0.69), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.68 (0.53), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 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 32 residues out of total 60 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.062 Fit side-chains REVERT: B 463 ASN cc_start: 0.5745 (p0) cc_final: 0.5360 (p0) REVERT: B 467 THR cc_start: 0.9134 (t) cc_final: 0.8427 (m) REVERT: A 451 ASN cc_start: 0.7867 (m-40) cc_final: 0.7452 (p0) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0621 time to fit residues: 2.2401 Evaluate side-chains 29 residues out of total 60 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.061 ------------------------------------------------------------------------------- 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: 0.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.0970 chunk 5 optimal weight: 0.6980 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 A 454 ASN A 464 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6329 moved from start: 0.9621 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= 0.169 Angle : 0.741 4.389 696 Z= 0.387 Chirality : 0.038 0.123 81 Planarity : 0.002 0.007 90 Dihedral : 6.108 17.285 69 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.67 % Favored : 73.33 % Rotamer: Outliers : 1.67 % Allowed : 1.67 % 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: -6.16 (0.70), 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 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 34 residues out of total 60 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.061 Fit side-chains REVERT: B 451 ASN cc_start: 0.7802 (m110) cc_final: 0.6753 (t0) REVERT: B 467 THR cc_start: 0.9164 (t) cc_final: 0.8351 (m) REVERT: A 451 ASN cc_start: 0.7842 (m-40) cc_final: 0.7458 (p0) outliers start: 1 outliers final: 0 residues processed: 34 average time/residue: 0.0485 time to fit residues: 1.8741 Evaluate side-chains 29 residues out of total 60 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.0980 chunk 2 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 overall best weight: 0.4313 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 464 ASN A 469 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6261 moved from start: 0.9981 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= 0.158 Angle : 0.748 4.453 696 Z= 0.388 Chirality : 0.038 0.120 81 Planarity : 0.003 0.012 90 Dihedral : 5.674 13.670 69 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.00 % Favored : 75.00 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -6.29 (0.67), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.78 (0.51), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 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 32 residues out of total 60 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.063 Fit side-chains REVERT: B 451 ASN cc_start: 0.7617 (m110) cc_final: 0.7012 (t0) REVERT: B 467 THR cc_start: 0.9167 (t) cc_final: 0.8390 (m) REVERT: A 451 ASN cc_start: 0.8050 (m-40) cc_final: 0.7613 (p0) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0562 time to fit residues: 2.0363 Evaluate side-chains 27 residues out of total 60 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.062 ------------------------------------------------------------------------------- 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: 0.4980 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 0.2980 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6313 moved from start: 1.0153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 513 Z= 0.177 Angle : 0.785 4.958 696 Z= 0.406 Chirality : 0.040 0.122 81 Planarity : 0.003 0.008 90 Dihedral : 5.688 15.388 69 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.67 % Favored : 73.33 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -6.08 (0.67), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.63 (0.51), 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 32 residues out of total 60 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.064 Fit side-chains REVERT: B 451 ASN cc_start: 0.7407 (m110) cc_final: 0.6663 (t0) REVERT: B 467 THR cc_start: 0.9153 (t) cc_final: 0.8374 (m) REVERT: A 451 ASN cc_start: 0.7991 (m-40) cc_final: 0.7408 (p0) REVERT: C 456 SER cc_start: 0.8002 (t) cc_final: 0.7744 (t) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0571 time to fit residues: 2.0702 Evaluate side-chains 27 residues out of total 60 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 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: 0.5980 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 0.0070 chunk 5 optimal weight: 1.9990 overall best weight: 0.5343 ------------------------------------------------------------------------------- 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 = 0.5213 r_free = 0.5213 target = 0.321994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.5384 r_free = 0.5384 target = 0.245792 restraints weight = 1008.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.5384 r_free = 0.5384 target = 0.245789 restraints weight = 1080.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5384 r_free = 0.5384 target = 0.245787 restraints weight = 1080.414| |-----------------------------------------------------------------------------| r_work (final): 0.4873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6210 moved from start: 1.0415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 513 Z= 0.168 Angle : 0.774 4.911 696 Z= 0.401 Chirality : 0.039 0.126 81 Planarity : 0.002 0.008 90 Dihedral : 5.566 16.281 69 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.67 % Favored : 73.33 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -6.05 (0.70), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.60 (0.53), 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: 572.41 seconds wall clock time: 10 minutes 54.23 seconds (654.23 seconds total)