Starting phenix.real_space_refine on Thu Jul 18 16:56:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ku5_23034/07_2024/7ku5_23034_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ku5_23034/07_2024/7ku5_23034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ku5_23034/07_2024/7ku5_23034.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ku5_23034/07_2024/7ku5_23034.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ku5_23034/07_2024/7ku5_23034_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ku5_23034/07_2024/7ku5_23034_neut.cif" } resolution = 3.76 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= 0.153 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: 5 Type Number sf(0) Gaussians Mg 3 5.21 5 S 1 5.16 5 C 512 2.51 5 N 125 2.21 5 O 109 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "O ARG 61": "NH1" <-> "NH2" Residue "O ARG 62": "NH1" <-> "NH2" Residue "O TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 750 Number of models: 1 Model: "" Number of chains: 2 Chain: "O" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 655 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 81} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "O" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 95 Unusual residues: {'BCR': 1, 'CLA': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'BCR:plan-2': 1, 'CLA:plan-2': 3, 'CLA:plan-3': 3, 'CLA:plan-4': 3, 'CLA:plan-5': 3, 'CLA:plan-6': 3, 'BCR:plan-5': 1, 'BCR:plan-4': 1, 'BCR:plan-7': 1, 'BCR:plan-6': 1, 'BCR:plan-3': 1, 'BCR:plan-8': 1} Unresolved non-hydrogen planarities: 91 Time building chain proxies: 1.45, per 1000 atoms: 1.93 Number of scatterers: 750 At special positions: 0 Unit cell: (52, 35.36, 62.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 1 16.00 Mg 3 11.99 O 109 8.00 N 125 7.00 C 512 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 - 3.50 Amino acid : False - 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: 0.28 Conformation dependent library (CDL) restraints added in 123.7 milliseconds 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 150 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 0 sheets defined 56.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'O' and resid 65 through 73 Processing helix chain 'O' and resid 83 through 87 removed outlier: 4.109A pdb=" N SER O 87 " --> pdb=" O ASN O 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 95 through 101 removed outlier: 3.623A pdb=" N GLU O 99 " --> pdb=" O SER O 95 " (cutoff:3.500A) Processing helix chain 'O' and resid 112 through 128 removed outlier: 4.374A pdb=" N TRP O 116 " --> pdb=" O PRO O 112 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL O 118 " --> pdb=" O TRP O 114 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL O 122 " --> pdb=" O VAL O 118 " (cutoff:3.500A) Processing helix chain 'O' and resid 129 through 140 removed outlier: 3.503A pdb=" N ILE O 133 " --> pdb=" O THR O 129 " (cutoff:3.500A) 25 hydrogen bonds defined for protein. 72 hydrogen bond angles 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: 0.17 Time building geometry restraints manager: 0.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.40: 335 1.40 - 1.57: 450 1.57 - 1.75: 0 1.75 - 1.92: 2 1.92 - 2.09: 12 Bond restraints: 799 Sorted by residual: bond pdb=" C GLY O 106 " pdb=" N PRO O 107 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.93e+00 bond pdb=" N THR O 105 " pdb=" CA THR O 105 " ideal model delta sigma weight residual 1.462 1.489 -0.027 1.48e-02 4.57e+03 3.42e+00 bond pdb=" N TRP O 114 " pdb=" CA TRP O 114 " ideal model delta sigma weight residual 1.457 1.481 -0.024 1.29e-02 6.01e+03 3.33e+00 bond pdb=" C25 BCR O 301 " pdb=" C30 BCR O 301 " ideal model delta sigma weight residual 1.532 1.496 0.036 2.00e-02 2.50e+03 3.16e+00 bond pdb=" CB TRP O 114 " pdb=" CG TRP O 114 " ideal model delta sigma weight residual 1.498 1.452 0.046 3.10e-02 1.04e+03 2.25e+00 ... (remaining 794 not shown) Histogram of bond angle deviations from ideal: 86.08 - 104.30: 34 104.30 - 122.52: 916 122.52 - 140.73: 174 140.73 - 158.95: 3 158.95 - 177.17: 6 Bond angle restraints: 1133 Sorted by residual: angle pdb=" C PRO O 104 " pdb=" N THR O 105 " pdb=" CA THR O 105 " ideal model delta sigma weight residual 122.61 129.47 -6.86 1.56e+00 4.11e-01 1.93e+01 angle pdb=" C TRP O 114 " pdb=" CA TRP O 114 " pdb=" CB TRP O 114 " ideal model delta sigma weight residual 110.42 102.99 7.43 1.99e+00 2.53e-01 1.39e+01 angle pdb=" CA LEU O 91 " pdb=" CB LEU O 91 " pdb=" CG LEU O 91 " ideal model delta sigma weight residual 116.30 128.87 -12.57 3.50e+00 8.16e-02 1.29e+01 angle pdb=" N TRP O 114 " pdb=" CA TRP O 114 " pdb=" CB TRP O 114 " ideal model delta sigma weight residual 110.49 116.45 -5.96 1.69e+00 3.50e-01 1.24e+01 angle pdb=" N TRP O 114 " pdb=" CA TRP O 114 " pdb=" C TRP O 114 " ideal model delta sigma weight residual 110.80 118.02 -7.22 2.13e+00 2.20e-01 1.15e+01 ... (remaining 1128 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 332 17.20 - 34.39: 36 34.39 - 51.59: 5 51.59 - 68.79: 0 68.79 - 85.98: 1 Dihedral angle restraints: 374 sinusoidal: 136 harmonic: 238 Sorted by residual: dihedral pdb=" CA GLY O 106 " pdb=" C GLY O 106 " pdb=" N PRO O 107 " pdb=" CA PRO O 107 " ideal model delta harmonic sigma weight residual -180.00 -155.26 -24.74 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA TRP O 74 " pdb=" C TRP O 74 " pdb=" N LEU O 75 " pdb=" CA LEU O 75 " ideal model delta harmonic sigma weight residual 180.00 161.89 18.11 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA PHE O 92 " pdb=" C PHE O 92 " pdb=" N LEU O 93 " pdb=" CA LEU O 93 " ideal model delta harmonic sigma weight residual 180.00 162.00 18.00 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 371 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 49 0.046 - 0.091: 33 0.091 - 0.137: 10 0.137 - 0.182: 2 0.182 - 0.228: 3 Chirality restraints: 97 Sorted by residual: chirality pdb=" CA TRP O 114 " pdb=" N TRP O 114 " pdb=" C TRP O 114 " pdb=" CB TRP O 114 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA LEU O 91 " pdb=" N LEU O 91 " pdb=" C LEU O 91 " pdb=" CB LEU O 91 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.32e-01 chirality pdb=" CA THR O 105 " pdb=" N THR O 105 " pdb=" C THR O 105 " pdb=" CB THR O 105 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.57e-01 ... (remaining 94 not shown) Planarity restraints: 153 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND CLA O 201 " 0.064 2.00e-02 2.50e+03 4.55e-02 3.10e+01 pdb=" C1A CLA O 201 " -0.028 2.00e-02 2.50e+03 pdb=" C3D CLA O 201 " -0.045 2.00e-02 2.50e+03 pdb=" C4D CLA O 201 " -0.039 2.00e-02 2.50e+03 pdb=" CBD CLA O 201 " 0.061 2.00e-02 2.50e+03 pdb=" CHA CLA O 201 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP O 114 " 0.037 2.00e-02 2.50e+03 2.78e-02 1.93e+01 pdb=" CG TRP O 114 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP O 114 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP O 114 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP O 114 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP O 114 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP O 114 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP O 114 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP O 114 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP O 114 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A CLA O 203 " -0.019 2.00e-02 2.50e+03 3.56e-02 1.90e+01 pdb=" C2A CLA O 203 " 0.058 2.00e-02 2.50e+03 pdb=" C4A CLA O 203 " -0.032 2.00e-02 2.50e+03 pdb=" CHA CLA O 203 " -0.023 2.00e-02 2.50e+03 pdb=" NA CLA O 203 " -0.026 2.00e-02 2.50e+03 pdb="MG CLA O 203 " 0.041 2.00e-02 2.50e+03 ... (remaining 150 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 252 2.92 - 3.41: 653 3.41 - 3.91: 1118 3.91 - 4.40: 1191 4.40 - 4.90: 1854 Nonbonded interactions: 5068 Sorted by model distance: nonbonded pdb=" NH1 ARG O 61 " pdb=" OE1 GLN O 132 " model vdw 2.420 2.520 nonbonded pdb=" NZ LYS O 136 " pdb=" OD2 ASP O 140 " model vdw 2.502 2.520 nonbonded pdb=" O LEU O 75 " pdb=" OG SER O 79 " model vdw 2.510 2.440 nonbonded pdb=" O LEU O 91 " pdb=" N SER O 95 " model vdw 2.525 2.520 nonbonded pdb=" O ASP O 63 " pdb=" N SER O 65 " model vdw 2.582 2.520 ... (remaining 5063 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.180 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 8.560 Find NCS groups from input model: 0.000 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6454 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 : 0.006 0.052 799 Z= 0.382 Angle : 1.290 12.573 1133 Z= 0.648 Chirality : 0.068 0.228 97 Planarity : 0.013 0.066 153 Dihedral : 14.852 85.984 224 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.79 % Favored : 87.21 % 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: -5.41 (0.71), residues: 86 helix: -4.07 (0.40), residues: 40 sheet: None (None), residues: 0 loop : -3.17 (0.90), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.003 TRP O 114 HIS 0.002 0.001 HIS O 121 PHE 0.022 0.002 PHE O 92 TYR 0.008 0.002 TYR O 142 ARG 0.024 0.008 ARG O 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.068 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1950 time to fit residues: 3.1752 Evaluate side-chains 12 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.3485 ------------------------------------------------------------------------------- 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: 0.6692 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 799 Z= 0.214 Angle : 0.691 5.804 1133 Z= 0.342 Chirality : 0.049 0.149 97 Planarity : 0.006 0.050 153 Dihedral : 6.868 23.444 99 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 3.33 % Allowed : 8.33 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.05 (0.85), residues: 86 helix: -2.69 (0.59), residues: 44 sheet: None (None), residues: 0 loop : -2.63 (1.08), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP O 114 HIS 0.001 0.000 HIS O 121 PHE 0.013 0.001 PHE O 92 TYR 0.006 0.002 TYR O 142 ARG 0.003 0.001 ARG O 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 15 time to evaluate : 0.075 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 15 average time/residue: 0.0462 time to fit residues: 0.8992 Evaluate side-chains 15 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 13 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain O residue 84 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 0.0770 chunk 2 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- 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: 0.6694 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 799 Z= 0.143 Angle : 0.601 6.032 1133 Z= 0.287 Chirality : 0.046 0.133 97 Planarity : 0.006 0.044 153 Dihedral : 6.116 20.775 99 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 3.33 % Allowed : 11.67 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.88), residues: 86 helix: -1.71 (0.64), residues: 45 sheet: None (None), residues: 0 loop : -2.75 (1.12), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP O 74 HIS 0.001 0.000 HIS O 121 PHE 0.014 0.001 PHE O 92 TYR 0.003 0.001 TYR O 142 ARG 0.001 0.000 ARG O 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 13 time to evaluate : 0.069 Fit side-chains REVERT: O 142 TYR cc_start: 0.7810 (m-80) cc_final: 0.7310 (m-80) outliers start: 2 outliers final: 1 residues processed: 13 average time/residue: 0.0559 time to fit residues: 0.9379 Evaluate side-chains 14 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 13 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 75 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 0.1980 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.6983 ------------------------------------------------------------------------------- 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: 0.6772 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 799 Z= 0.152 Angle : 0.599 5.917 1133 Z= 0.295 Chirality : 0.046 0.114 97 Planarity : 0.006 0.042 153 Dihedral : 6.027 19.337 99 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 3.33 % Allowed : 11.67 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.95), residues: 86 helix: -0.86 (0.73), residues: 46 sheet: None (None), residues: 0 loop : -2.48 (1.16), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 74 HIS 0.000 0.000 HIS O 121 PHE 0.011 0.001 PHE O 92 TYR 0.003 0.001 TYR O 142 ARG 0.001 0.000 ARG O 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 14 time to evaluate : 0.071 Fit side-chains REVERT: O 114 TRP cc_start: 0.6731 (m-90) cc_final: 0.6349 (m-10) REVERT: O 142 TYR cc_start: 0.7828 (m-80) cc_final: 0.7396 (m-80) outliers start: 2 outliers final: 0 residues processed: 14 average time/residue: 0.0600 time to fit residues: 1.0430 Evaluate side-chains 14 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.0170 chunk 2 optimal weight: 0.0670 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 overall best weight: 0.4950 ------------------------------------------------------------------------------- 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: 0.6748 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 799 Z= 0.137 Angle : 0.580 5.778 1133 Z= 0.276 Chirality : 0.048 0.167 97 Planarity : 0.006 0.041 153 Dihedral : 5.829 19.784 99 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.63 % Favored : 88.37 % Rotamer: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % 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: -1.78 (0.99), residues: 86 helix: -0.45 (0.75), residues: 45 sheet: None (None), residues: 0 loop : -2.03 (1.23), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 74 HIS 0.001 0.000 HIS O 121 PHE 0.009 0.001 PHE O 92 TYR 0.002 0.001 TYR O 142 ARG 0.001 0.000 ARG O 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.076 Fit side-chains REVERT: O 91 LEU cc_start: 0.7876 (pp) cc_final: 0.7618 (pp) REVERT: O 114 TRP cc_start: 0.6806 (m-90) cc_final: 0.6408 (m-10) REVERT: O 142 TYR cc_start: 0.7785 (m-80) cc_final: 0.7378 (m-80) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0594 time to fit residues: 1.1764 Evaluate side-chains 16 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.0970 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.8733 ------------------------------------------------------------------------------- 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: 0.6842 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 799 Z= 0.159 Angle : 0.595 6.042 1133 Z= 0.291 Chirality : 0.048 0.119 97 Planarity : 0.006 0.040 153 Dihedral : 5.997 19.895 99 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 1.67 % Allowed : 20.00 % Favored : 78.33 % 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: -2.06 (0.96), residues: 86 helix: -0.44 (0.72), residues: 46 sheet: None (None), residues: 0 loop : -2.53 (1.19), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 74 HIS 0.001 0.001 HIS O 121 PHE 0.011 0.002 PHE O 92 TYR 0.005 0.001 TYR O 142 ARG 0.001 0.000 ARG O 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 12 time to evaluate : 0.075 Fit side-chains REVERT: O 114 TRP cc_start: 0.7088 (m-90) cc_final: 0.6401 (m-10) REVERT: O 142 TYR cc_start: 0.7893 (m-80) cc_final: 0.7491 (m-80) outliers start: 1 outliers final: 1 residues processed: 13 average time/residue: 0.0586 time to fit residues: 0.9657 Evaluate side-chains 13 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 12 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 82 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.1980 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 overall best weight: 1.2233 ------------------------------------------------------------------------------- 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: 0.6918 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 799 Z= 0.179 Angle : 0.620 5.873 1133 Z= 0.300 Chirality : 0.051 0.137 97 Planarity : 0.006 0.040 153 Dihedral : 6.056 19.762 99 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 1.67 % Allowed : 18.33 % Favored : 80.00 % 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: -1.81 (0.99), residues: 86 helix: -0.29 (0.74), residues: 46 sheet: None (None), residues: 0 loop : -2.34 (1.23), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 74 HIS 0.001 0.000 HIS O 121 PHE 0.009 0.001 PHE O 135 TYR 0.005 0.001 TYR O 142 ARG 0.002 0.000 ARG O 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 11 time to evaluate : 0.074 Fit side-chains REVERT: O 114 TRP cc_start: 0.7191 (m-90) cc_final: 0.4602 (p-90) REVERT: O 142 TYR cc_start: 0.7932 (m-80) cc_final: 0.7481 (m-80) outliers start: 1 outliers final: 1 residues processed: 12 average time/residue: 0.0579 time to fit residues: 0.8923 Evaluate side-chains 12 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 11 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 82 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 0.0270 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 overall best weight: 0.6053 ------------------------------------------------------------------------------- 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: 0.6848 moved from start: 0.4447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 799 Z= 0.150 Angle : 0.660 9.482 1133 Z= 0.298 Chirality : 0.047 0.148 97 Planarity : 0.006 0.041 153 Dihedral : 5.990 18.741 99 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 1.67 % Allowed : 18.33 % Favored : 80.00 % 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: -1.71 (0.98), residues: 86 helix: -0.14 (0.75), residues: 46 sheet: None (None), residues: 0 loop : -2.39 (1.20), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 74 HIS 0.000 0.000 HIS O 102 PHE 0.009 0.001 PHE O 92 TYR 0.002 0.001 TYR O 142 ARG 0.001 0.000 ARG O 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.076 Fit side-chains REVERT: O 91 LEU cc_start: 0.7971 (pp) cc_final: 0.7723 (pp) REVERT: O 114 TRP cc_start: 0.7091 (m-90) cc_final: 0.4578 (p-90) REVERT: O 142 TYR cc_start: 0.7799 (m-80) cc_final: 0.7366 (m-80) outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.0598 time to fit residues: 1.1865 Evaluate side-chains 16 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 82 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 5 optimal weight: 0.2980 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.7733 ------------------------------------------------------------------------------- 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: 0.6844 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 799 Z= 0.160 Angle : 0.666 9.280 1133 Z= 0.304 Chirality : 0.048 0.139 97 Planarity : 0.006 0.039 153 Dihedral : 5.837 18.608 99 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.63 % Favored : 88.37 % Rotamer: Outliers : 1.67 % Allowed : 20.00 % Favored : 78.33 % 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: -1.97 (0.98), residues: 86 helix: -0.40 (0.78), residues: 44 sheet: None (None), residues: 0 loop : -2.36 (1.15), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 74 HIS 0.001 0.000 HIS O 121 PHE 0.008 0.001 PHE O 92 TYR 0.004 0.001 TYR O 142 ARG 0.001 0.000 ARG O 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 14 time to evaluate : 0.075 Fit side-chains REVERT: O 91 LEU cc_start: 0.7992 (pp) cc_final: 0.7739 (pp) REVERT: O 114 TRP cc_start: 0.7088 (m-90) cc_final: 0.4547 (p-90) REVERT: O 142 TYR cc_start: 0.7911 (m-80) cc_final: 0.7483 (m-80) outliers start: 1 outliers final: 1 residues processed: 15 average time/residue: 0.0461 time to fit residues: 0.8881 Evaluate side-chains 15 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 14 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 82 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 0.0980 chunk 3 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 0.3980 chunk 6 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 overall best weight: 1.5483 ------------------------------------------------------------------------------- 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: 0.6963 moved from start: 0.4942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 799 Z= 0.218 Angle : 0.715 9.206 1133 Z= 0.336 Chirality : 0.051 0.131 97 Planarity : 0.006 0.039 153 Dihedral : 6.179 17.922 99 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.79 % Favored : 87.21 % Rotamer: Outliers : 1.67 % Allowed : 18.33 % Favored : 80.00 % 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: -1.92 (0.98), residues: 86 helix: -0.28 (0.76), residues: 46 sheet: None (None), residues: 0 loop : -2.54 (1.16), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 74 HIS 0.001 0.000 HIS O 121 PHE 0.011 0.002 PHE O 135 TYR 0.006 0.002 TYR O 142 ARG 0.002 0.001 ARG O 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 14 time to evaluate : 0.073 Fit side-chains REVERT: O 114 TRP cc_start: 0.7203 (m-90) cc_final: 0.4603 (p-90) REVERT: O 142 TYR cc_start: 0.8080 (m-80) cc_final: 0.7607 (m-80) outliers start: 1 outliers final: 1 residues processed: 14 average time/residue: 0.0579 time to fit residues: 1.0184 Evaluate side-chains 13 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 12 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 82 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.1483 ------------------------------------------------------------------------------- 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 = 0.4120 r_free = 0.4120 target = 0.175429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.167269 restraints weight = 1518.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.169373 restraints weight = 696.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.170592 restraints weight = 395.603| |-----------------------------------------------------------------------------| r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 799 Z= 0.181 Angle : 0.685 9.471 1133 Z= 0.315 Chirality : 0.050 0.148 97 Planarity : 0.006 0.039 153 Dihedral : 6.046 17.331 99 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.79 % Favored : 87.21 % Rotamer: Outliers : 1.67 % Allowed : 23.33 % Favored : 75.00 % 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: -2.11 (0.97), residues: 86 helix: -0.39 (0.79), residues: 44 sheet: None (None), residues: 0 loop : -2.59 (1.10), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 74 HIS 0.001 0.000 HIS O 121 PHE 0.009 0.001 PHE O 92 TYR 0.004 0.001 TYR O 142 ARG 0.002 0.001 ARG O 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 571.10 seconds wall clock time: 10 minutes 53.70 seconds (653.70 seconds total)