Starting phenix.real_space_refine on Thu Dec 7 15:49:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ku5_23034/12_2023/7ku5_23034_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ku5_23034/12_2023/7ku5_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_23034/12_2023/7ku5_23034.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ku5_23034/12_2023/7ku5_23034.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ku5_23034/12_2023/7ku5_23034_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ku5_23034/12_2023/7ku5_23034_updated.pdb" } 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-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 750 Number of models: 1 Model: "" Number of chains: 1 Chain: "O" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 750 Unusual residues: {'BCR': 1, 'CLA': 3} Classifications: {'peptide': 88, 'undetermined': 4} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 81, None: 4} Not linked: pdbres="TRP O 143 " pdbres="CLA O 201 " Not linked: pdbres="CLA O 201 " pdbres="CLA O 202 " Not linked: pdbres="CLA O 202 " pdbres="CLA O 203 " Not linked: pdbres="CLA O 203 " pdbres="BCR O 301 " Unresolved non-hydrogen bonds: 184 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'BCR:plan-6': 1, 'BCR:plan-2': 1, 'BCR:plan-5': 1, 'CLA:plan-2': 3, 'CLA:plan-3': 3, 'CLA:plan-4': 3, 'CLA:plan-5': 3, 'CLA:plan-6': 3, 'BCR:plan-4': 1, 'PHE:plan': 2, 'GLU:plan': 1, 'BCR:plan-7': 1, 'ARG:plan': 1, 'BCR:plan-3': 1, 'BCR:plan-8': 1} Unresolved non-hydrogen planarities: 112 Time building chain proxies: 1.26, per 1000 atoms: 1.68 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: 0.29 Conformation dependent library (CDL) restraints added in 252.0 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... running ksdssp... Secondary structure from input PDB file: 5 helices and 0 sheets defined 45.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'O' and resid 66 through 72 Processing helix chain 'O' and resid 84 through 86 No H-bonds generated for 'chain 'O' and resid 84 through 86' Processing helix chain 'O' and resid 96 through 100 Processing helix chain 'O' and resid 113 through 127 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 130 through 139 19 hydrogen bonds defined for protein. 57 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: 0.15 Time building geometry restraints manager: 0.31 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: 256 2.92 - 3.41: 658 3.41 - 3.91: 1128 3.91 - 4.40: 1196 4.40 - 4.90: 1854 Nonbonded interactions: 5092 Sorted by model distance: nonbonded pdb=" NH1 ARG O 61 " pdb=" OE1 GLN O 132 " model vdw 2.420 2.520 nonbonded pdb=" O SER O 65 " pdb=" N PHE O 69 " model vdw 2.457 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 ... (remaining 5087 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: 1.030 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: 4.400 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.590 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.010 ------------------------------------------------------------------------------- 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= 0.369 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 : 0.077 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1534 time to fit residues: 2.5210 Evaluate side-chains 12 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.078 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.0270 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 overall best weight: 0.6055 ------------------------------------------------------------------------------- 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: 0.6532 moved from start: 0.1776 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= 0.155 Angle : 0.640 5.466 1133 Z= 0.308 Chirality : 0.047 0.167 97 Planarity : 0.006 0.050 153 Dihedral : 6.548 22.653 99 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.33 % Allowed : 10.00 % Favored : 86.67 % 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: -4.01 (0.84), residues: 86 helix: -2.73 (0.59), residues: 43 sheet: None (None), residues: 0 loop : -2.56 (1.06), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP O 114 HIS 0.001 0.000 HIS O 121 PHE 0.013 0.001 PHE O 92 TYR 0.004 0.001 TYR O 142 ARG 0.002 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 18 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 16 time to evaluate : 0.075 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 16 average time/residue: 0.1229 time to fit residues: 2.1918 Evaluate side-chains 17 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 15 time to evaluate : 0.074 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0144 time to fit residues: 0.1385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.6735 ------------------------------------------------------------------------------- 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: 0.6888 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 799 Z= 0.258 Angle : 0.697 6.200 1133 Z= 0.344 Chirality : 0.050 0.123 97 Planarity : 0.006 0.042 153 Dihedral : 6.414 20.934 99 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.79 % Favored : 87.21 % Rotamer: Outliers : 0.00 % Allowed : 15.00 % 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: -3.43 (0.83), residues: 86 helix: -2.07 (0.60), residues: 48 sheet: None (None), residues: 0 loop : -2.45 (1.11), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 116 HIS 0.002 0.001 HIS O 121 PHE 0.015 0.002 PHE O 92 TYR 0.011 0.003 TYR O 142 ARG 0.005 0.002 ARG O 62 *********************** 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 14 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.075 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0648 time to fit residues: 1.1133 Evaluate side-chains 12 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.074 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 0.0010 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- 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: 0.6811 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 799 Z= 0.152 Angle : 0.602 5.946 1133 Z= 0.281 Chirality : 0.045 0.113 97 Planarity : 0.005 0.040 153 Dihedral : 6.127 19.501 99 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 3.33 % Allowed : 16.67 % 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: -2.48 (0.94), residues: 86 helix: -1.27 (0.70), residues: 47 sheet: None (None), residues: 0 loop : -2.05 (1.21), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 74 HIS 0.000 0.000 HIS O 102 PHE 0.011 0.001 PHE O 92 TYR 0.001 0.000 TYR O 142 ARG 0.001 0.000 ARG O 61 *********************** 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 : 0.076 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 16 average time/residue: 0.0590 time to fit residues: 1.1701 Evaluate side-chains 14 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 12 time to evaluate : 0.076 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0135 time to fit residues: 0.1365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 4 optimal weight: 0.4980 chunk 5 optimal weight: 0.3980 chunk 6 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 overall best weight: 0.6230 ------------------------------------------------------------------------------- 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: 0.6835 moved from start: 0.3927 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= 0.145 Angle : 0.587 5.781 1133 Z= 0.272 Chirality : 0.044 0.114 97 Planarity : 0.005 0.039 153 Dihedral : 5.825 18.956 99 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % 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: -2.11 (0.99), residues: 86 helix: -0.95 (0.75), residues: 47 sheet: None (None), residues: 0 loop : -1.90 (1.25), residues: 39 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 0.010 0.001 PHE O 92 TYR 0.002 0.001 TYR O 142 ARG 0.001 0.000 ARG O 62 *********************** 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 17 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.076 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0647 time to fit residues: 1.3381 Evaluate side-chains 15 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.077 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.0770 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 chunk 7 optimal weight: 0.0870 chunk 8 optimal weight: 3.9990 overall best weight: 1.2153 ------------------------------------------------------------------------------- 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: 0.6923 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 799 Z= 0.171 Angle : 0.697 9.465 1133 Z= 0.318 Chirality : 0.048 0.120 97 Planarity : 0.006 0.039 153 Dihedral : 6.154 18.695 99 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 3.33 % Allowed : 20.00 % Favored : 76.67 % 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: -1.78 (1.00), residues: 86 helix: -0.81 (0.74), residues: 47 sheet: None (None), residues: 0 loop : -1.56 (1.28), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 114 HIS 0.002 0.001 HIS O 102 PHE 0.009 0.002 PHE O 92 TYR 0.001 0.001 TYR O 142 ARG 0.001 0.001 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 15 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 13 time to evaluate : 0.065 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 14 average time/residue: 0.0639 time to fit residues: 1.1081 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 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0136 time to fit residues: 0.1376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 0.3980 chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 overall best weight: 0.7230 ------------------------------------------------------------------------------- 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: 0.6831 moved from start: 0.4795 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= 0.139 Angle : 0.638 8.675 1133 Z= 0.283 Chirality : 0.045 0.116 97 Planarity : 0.005 0.040 153 Dihedral : 5.937 18.417 99 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % 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: -1.34 (1.03), residues: 86 helix: -0.42 (0.76), residues: 47 sheet: None (None), residues: 0 loop : -1.41 (1.32), residues: 39 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 0.008 0.001 PHE O 92 TYR 0.002 0.001 TYR O 142 ARG 0.001 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 15 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.076 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0597 time to fit residues: 1.1132 Evaluate side-chains 14 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.074 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 0.0870 chunk 3 optimal weight: 0.0670 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 overall best weight: 0.4125 ------------------------------------------------------------------------------- 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: 0.6759 moved from start: 0.4790 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= 0.132 Angle : 0.642 9.202 1133 Z= 0.281 Chirality : 0.043 0.117 97 Planarity : 0.005 0.039 153 Dihedral : 5.719 17.886 99 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 0.00 % Allowed : 23.33 % Favored : 76.67 % 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: -1.34 (1.02), residues: 86 helix: -0.07 (0.77), residues: 43 sheet: None (None), residues: 0 loop : -1.77 (1.23), residues: 43 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 0.008 0.001 PHE O 92 TYR 0.001 0.000 TYR O 142 ARG 0.001 0.000 ARG O 138 *********************** 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 15 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.075 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0590 time to fit residues: 1.0995 Evaluate side-chains 15 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.075 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 0.2980 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 0.0670 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 overall best weight: 0.4653 ------------------------------------------------------------------------------- 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: 0.6758 moved from start: 0.4885 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= 0.131 Angle : 0.631 9.159 1133 Z= 0.273 Chirality : 0.043 0.115 97 Planarity : 0.005 0.039 153 Dihedral : 5.520 18.420 99 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 0.00 % Allowed : 25.00 % 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: -1.32 (1.01), residues: 86 helix: 0.03 (0.77), residues: 43 sheet: None (None), residues: 0 loop : -1.87 (1.20), residues: 43 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 0.008 0.001 PHE O 92 TYR 0.001 0.000 TYR O 142 ARG 0.001 0.000 ARG O 62 *********************** 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: 0 poor density : 15 time to evaluate : 0.073 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0602 time to fit residues: 1.1166 Evaluate side-chains 15 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.073 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 0.0270 chunk 3 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 0.3980 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 overall best weight: 0.4803 ------------------------------------------------------------------------------- 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: 0.6757 moved from start: 0.5027 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= 0.132 Angle : 0.632 9.192 1133 Z= 0.274 Chirality : 0.044 0.117 97 Planarity : 0.005 0.039 153 Dihedral : 5.549 18.547 99 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % 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: -1.36 (1.00), residues: 86 helix: 0.03 (0.77), residues: 43 sheet: None (None), residues: 0 loop : -1.92 (1.19), residues: 43 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 0.008 0.001 PHE O 92 TYR 0.001 0.000 TYR O 142 ARG 0.001 0.000 ARG O 138 ********************** 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 : 0.077 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 14 average time/residue: 0.0560 time to fit residues: 0.9940 Evaluate side-chains 15 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 14 time to evaluate : 0.069 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0133 time to fit residues: 0.1146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 0.2980 chunk 8 optimal weight: 4.9990 overall best weight: 0.6230 ------------------------------------------------------------------------------- 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 = 0.4121 r_free = 0.4121 target = 0.177774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.168774 restraints weight = 1594.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.170873 restraints weight = 833.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.172355 restraints weight = 517.033| |-----------------------------------------------------------------------------| r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.5075 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= 0.134 Angle : 0.632 9.067 1133 Z= 0.274 Chirality : 0.044 0.116 97 Planarity : 0.005 0.038 153 Dihedral : 5.454 18.617 99 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 0.00 % Allowed : 25.00 % 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: -1.35 (1.00), residues: 86 helix: 0.07 (0.77), residues: 43 sheet: None (None), residues: 0 loop : -1.96 (1.18), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP O 74 HIS 0.000 0.000 HIS O 121 PHE 0.008 0.001 PHE O 92 TYR 0.001 0.000 TYR O 142 ARG 0.000 0.000 ARG O 138 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 646.07 seconds wall clock time: 17 minutes 18.30 seconds (1038.30 seconds total)