Starting phenix.real_space_refine on Thu Dec 7 16:10:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y14_33556/12_2023/7y14_33556_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y14_33556/12_2023/7y14_33556.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y14_33556/12_2023/7y14_33556.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y14_33556/12_2023/7y14_33556.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y14_33556/12_2023/7y14_33556_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y14_33556/12_2023/7y14_33556_updated.pdb" } resolution = 3.2 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= -0.003 sd= 0.055 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 1431 2.51 5 N 342 2.21 5 O 350 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 99": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 2145 Number of models: 1 Model: "" Number of chains: 1 Chain: "R" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2145 Unusual residues: {'BAL': 1, 'PLM': 4} Classifications: {'peptide': 264, 'undetermined': 5} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PRE-BETA-TRANS': 1, 'PTRANS': 10, 'TRANS': 253, None: 4} Not linked: pdbres="BAL R1001 " pdbres="PLM R1002 " Not linked: pdbres="PLM R1002 " pdbres="PLM R1003 " Not linked: pdbres="PLM R1003 " pdbres="PLM R1004 " Not linked: pdbres="PLM R1004 " pdbres="PLM R1005 " Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Time building chain proxies: 1.72, per 1000 atoms: 0.80 Number of scatterers: 2145 At special positions: 0 Unit cell: (57.375, 68.175, 69.525, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 350 8.00 N 342 7.00 C 1431 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 164 " - pdb=" SG CYS R 175 " distance=2.03 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: 0.97 Conformation dependent library (CDL) restraints added in 435.8 milliseconds 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB BAL R1001 " Number of C-beta restraints generated: 512 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 9 helices and 0 sheets defined 74.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'R' and resid 23 through 51 removed outlier: 3.709A pdb=" N LEU R 28 " --> pdb=" O HIS R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 85 Processing helix chain 'R' and resid 96 through 128 removed outlier: 3.733A pdb=" N VAL R 127 " --> pdb=" O ARG R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 135 Processing helix chain 'R' and resid 141 through 164 Processing helix chain 'R' and resid 173 through 208 removed outlier: 4.983A pdb=" N THR R 191 " --> pdb=" O MET R 187 " (cutoff:3.500A) Proline residue: R 192 - end of helix Processing helix chain 'R' and resid 217 through 233 Processing helix chain 'R' and resid 235 through 241 Processing helix chain 'R' and resid 254 through 276 Proline residue: R 273 - end of helix 153 hydrogen bonds defined for protein. 459 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: 0.60 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 427 1.33 - 1.45: 506 1.45 - 1.57: 1230 1.57 - 1.69: 0 1.69 - 1.81: 33 Bond restraints: 2196 Sorted by residual: bond pdb=" C BAL R1001 " pdb=" OXT BAL R1001 " ideal model delta sigma weight residual 1.247 1.307 -0.060 2.00e-02 2.50e+03 8.85e+00 bond pdb=" C1 PLM R1002 " pdb=" C2 PLM R1002 " ideal model delta sigma weight residual 1.542 1.569 -0.027 2.00e-02 2.50e+03 1.86e+00 bond pdb=" C1 PLM R1004 " pdb=" C2 PLM R1004 " ideal model delta sigma weight residual 1.542 1.566 -0.024 2.00e-02 2.50e+03 1.45e+00 bond pdb=" CA BAL R1001 " pdb=" C BAL R1001 " ideal model delta sigma weight residual 1.525 1.500 0.025 2.10e-02 2.27e+03 1.40e+00 bond pdb=" C1 PLM R1003 " pdb=" C2 PLM R1003 " ideal model delta sigma weight residual 1.542 1.565 -0.023 2.00e-02 2.50e+03 1.35e+00 ... (remaining 2191 not shown) Histogram of bond angle deviations from ideal: 99.37 - 106.29: 60 106.29 - 113.21: 1200 113.21 - 120.13: 811 120.13 - 127.05: 862 127.05 - 133.97: 36 Bond angle restraints: 2969 Sorted by residual: angle pdb=" CA BAL R1001 " pdb=" C BAL R1001 " pdb=" OXT BAL R1001 " ideal model delta sigma weight residual 120.80 113.34 7.46 1.70e+00 3.46e-01 1.92e+01 angle pdb=" N BAL R1001 " pdb=" CB BAL R1001 " pdb=" CA BAL R1001 " ideal model delta sigma weight residual 110.40 114.96 -4.56 1.50e+00 4.44e-01 9.23e+00 angle pdb=" N MET R 79 " pdb=" CA MET R 79 " pdb=" CB MET R 79 " ideal model delta sigma weight residual 110.16 113.87 -3.71 1.48e+00 4.57e-01 6.30e+00 angle pdb=" CA TRP R 144 " pdb=" CB TRP R 144 " pdb=" CG TRP R 144 " ideal model delta sigma weight residual 113.60 118.12 -4.52 1.90e+00 2.77e-01 5.65e+00 angle pdb=" C ALA R 143 " pdb=" N TRP R 144 " pdb=" CA TRP R 144 " ideal model delta sigma weight residual 121.14 117.15 3.99 1.75e+00 3.27e-01 5.19e+00 ... (remaining 2964 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.25: 1146 16.25 - 32.51: 131 32.51 - 48.76: 20 48.76 - 65.01: 3 65.01 - 81.27: 1 Dihedral angle restraints: 1301 sinusoidal: 519 harmonic: 782 Sorted by residual: dihedral pdb=" CB GLU R 99 " pdb=" CG GLU R 99 " pdb=" CD GLU R 99 " pdb=" OE1 GLU R 99 " ideal model delta sinusoidal sigma weight residual 0.00 81.27 -81.27 1 3.00e+01 1.11e-03 9.05e+00 dihedral pdb=" CB MET R 180 " pdb=" CG MET R 180 " pdb=" SD MET R 180 " pdb=" CE MET R 180 " ideal model delta sinusoidal sigma weight residual 60.00 110.60 -50.60 3 1.50e+01 4.44e-03 8.92e+00 dihedral pdb=" CA LEU R 228 " pdb=" CB LEU R 228 " pdb=" CG LEU R 228 " pdb=" CD1 LEU R 228 " ideal model delta sinusoidal sigma weight residual 180.00 134.54 45.46 3 1.50e+01 4.44e-03 8.17e+00 ... (remaining 1298 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 224 0.031 - 0.063: 95 0.063 - 0.094: 22 0.094 - 0.125: 5 0.125 - 0.157: 5 Chirality restraints: 351 Sorted by residual: chirality pdb=" CA TRP R 144 " pdb=" N TRP R 144 " pdb=" C TRP R 144 " pdb=" CB TRP R 144 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.13e-01 chirality pdb=" CA MET R 79 " pdb=" N MET R 79 " pdb=" C MET R 79 " pdb=" CB MET R 79 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.99e-01 chirality pdb=" CA THR R 191 " pdb=" N THR R 191 " pdb=" C THR R 191 " pdb=" CB THR R 191 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.62e-01 ... (remaining 348 not shown) Planarity restraints: 348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 144 " -0.020 2.00e-02 2.50e+03 1.58e-02 6.20e+00 pdb=" CG TRP R 144 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP R 144 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP R 144 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 144 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 144 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 144 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 144 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 144 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP R 144 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN R 88 " 0.038 5.00e-02 4.00e+02 5.86e-02 5.49e+00 pdb=" N PRO R 89 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO R 89 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 89 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN R 215 " -0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO R 216 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO R 216 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 216 " -0.021 5.00e-02 4.00e+02 ... (remaining 345 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 631 2.83 - 3.35: 2163 3.35 - 3.86: 3652 3.86 - 4.38: 4016 4.38 - 4.90: 7066 Nonbonded interactions: 17528 Sorted by model distance: nonbonded pdb=" OD2 ASP R 179 " pdb=" N BAL R1001 " model vdw 2.312 2.520 nonbonded pdb=" OH TYR R 109 " pdb=" O SER R 234 " model vdw 2.332 2.440 nonbonded pdb=" O THR R 191 " pdb=" OG1 THR R 195 " model vdw 2.460 2.440 nonbonded pdb=" O ARG R 55 " pdb=" ND1 HIS R 57 " model vdw 2.461 2.520 nonbonded pdb=" O GLY R 41 " pdb=" ND2 ASN R 45 " model vdw 2.471 2.520 ... (remaining 17523 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.350 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: 6.660 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.320 Find NCS groups from input model: 0.060 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 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 : 0.004 0.060 2196 Z= 0.264 Angle : 0.663 7.456 2969 Z= 0.351 Chirality : 0.039 0.157 351 Planarity : 0.005 0.059 348 Dihedral : 13.603 81.268 786 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.39 % 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: 2.46 (0.56), residues: 262 helix: 2.33 (0.37), residues: 207 sheet: None (None), residues: 0 loop : -1.20 (1.01), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP R 144 HIS 0.002 0.001 HIS R 98 PHE 0.022 0.002 PHE R 75 TYR 0.012 0.002 TYR R 106 ARG 0.003 0.000 ARG R 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.229 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1051 time to fit residues: 4.9358 Evaluate side-chains 31 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.245 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7309 moved from start: 0.0508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2196 Z= 0.200 Angle : 0.539 6.576 2969 Z= 0.272 Chirality : 0.037 0.153 351 Planarity : 0.005 0.055 348 Dihedral : 7.349 58.949 342 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.87 % Allowed : 4.76 % Favored : 94.37 % Cbeta Deviations : 0.39 % 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: 2.63 (0.56), residues: 262 helix: 2.45 (0.37), residues: 209 sheet: None (None), residues: 0 loop : -1.27 (1.03), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 144 HIS 0.002 0.001 HIS R 98 PHE 0.021 0.002 PHE R 75 TYR 0.015 0.002 TYR R 245 ARG 0.002 0.000 ARG R 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.205 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 34 average time/residue: 0.0926 time to fit residues: 4.0588 Evaluate side-chains 33 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.198 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0227 time to fit residues: 0.3171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 6 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 25 optimal weight: 0.0050 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 12 optimal weight: 0.3980 chunk 2 optimal weight: 0.3980 chunk 11 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 overall best weight: 0.4394 ------------------------------------------------------------------------------- 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: 0.7270 moved from start: 0.0741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2196 Z= 0.142 Angle : 0.493 6.370 2969 Z= 0.247 Chirality : 0.036 0.150 351 Planarity : 0.005 0.052 348 Dihedral : 6.890 59.038 342 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.30 % Allowed : 8.23 % Favored : 90.48 % Cbeta Deviations : 0.39 % 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: 2.90 (0.57), residues: 262 helix: 2.73 (0.38), residues: 207 sheet: None (None), residues: 0 loop : -1.45 (0.98), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 144 HIS 0.001 0.000 HIS R 98 PHE 0.013 0.001 PHE R 75 TYR 0.017 0.002 TYR R 245 ARG 0.001 0.000 ARG R 262 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.237 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 34 average time/residue: 0.1132 time to fit residues: 4.9521 Evaluate side-chains 33 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.228 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0247 time to fit residues: 0.3645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 23 optimal weight: 0.4980 chunk 25 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 6 optimal weight: 0.2980 chunk 20 optimal weight: 0.7980 chunk 14 optimal weight: 0.0970 chunk 0 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.0030 overall best weight: 0.3188 ------------------------------------------------------------------------------- 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: 0.7245 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2196 Z= 0.128 Angle : 0.472 6.335 2969 Z= 0.236 Chirality : 0.035 0.150 351 Planarity : 0.004 0.051 348 Dihedral : 6.507 57.228 342 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.87 % Allowed : 9.96 % Favored : 89.18 % Cbeta Deviations : 0.39 % 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: 3.01 (0.57), residues: 262 helix: 2.82 (0.37), residues: 207 sheet: None (None), residues: 0 loop : -1.48 (0.97), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 144 HIS 0.001 0.000 HIS R 98 PHE 0.014 0.001 PHE R 75 TYR 0.017 0.002 TYR R 245 ARG 0.001 0.000 ARG R 262 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.231 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 34 average time/residue: 0.1033 time to fit residues: 4.5134 Evaluate side-chains 34 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.242 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 6 optimal weight: 0.0870 chunk 8 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 0.0470 chunk 25 optimal weight: 0.3980 chunk 20 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 overall best weight: 0.3656 ------------------------------------------------------------------------------- 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: 0.7242 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2196 Z= 0.131 Angle : 0.487 6.295 2969 Z= 0.241 Chirality : 0.035 0.149 351 Planarity : 0.004 0.049 348 Dihedral : 6.427 55.864 342 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.87 % Allowed : 11.69 % Favored : 87.45 % Cbeta Deviations : 0.39 % 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: 3.10 (0.57), residues: 262 helix: 2.86 (0.37), residues: 208 sheet: None (None), residues: 0 loop : -1.44 (0.98), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 144 HIS 0.001 0.000 HIS R 98 PHE 0.013 0.001 PHE R 75 TYR 0.018 0.002 TYR R 245 ARG 0.001 0.000 ARG R 262 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.232 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 35 average time/residue: 0.1008 time to fit residues: 4.5238 Evaluate side-chains 34 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.238 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 2 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 14 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 285 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2196 Z= 0.199 Angle : 0.528 6.845 2969 Z= 0.266 Chirality : 0.037 0.150 351 Planarity : 0.005 0.048 348 Dihedral : 6.981 54.934 342 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.30 % Allowed : 14.29 % Favored : 84.42 % Cbeta Deviations : 0.39 % 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: 2.96 (0.57), residues: 262 helix: 2.71 (0.37), residues: 209 sheet: None (None), residues: 0 loop : -1.31 (1.04), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 144 HIS 0.002 0.001 HIS R 98 PHE 0.017 0.001 PHE R 75 TYR 0.019 0.002 TYR R 245 ARG 0.002 0.000 ARG R 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 0.212 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 32 average time/residue: 0.1083 time to fit residues: 4.4646 Evaluate side-chains 33 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.245 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0452 time to fit residues: 0.4047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 14 optimal weight: 0.0370 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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: 0.7293 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2196 Z= 0.173 Angle : 0.527 6.786 2969 Z= 0.263 Chirality : 0.036 0.148 351 Planarity : 0.004 0.047 348 Dihedral : 6.871 58.433 342 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.43 % Allowed : 15.58 % Favored : 83.98 % Cbeta Deviations : 0.39 % 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: 2.97 (0.57), residues: 262 helix: 2.71 (0.37), residues: 209 sheet: None (None), residues: 0 loop : -1.28 (1.03), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 144 HIS 0.002 0.000 HIS R 98 PHE 0.021 0.001 PHE R 75 TYR 0.019 0.002 TYR R 245 ARG 0.002 0.000 ARG R 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.244 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 35 average time/residue: 0.1008 time to fit residues: 4.5500 Evaluate side-chains 35 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 0.207 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0241 time to fit residues: 0.3343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 23 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 14 optimal weight: 0.0370 chunk 10 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2196 Z= 0.162 Angle : 0.529 6.517 2969 Z= 0.264 Chirality : 0.036 0.144 351 Planarity : 0.004 0.047 348 Dihedral : 6.807 59.640 342 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.00 % Allowed : 16.88 % Favored : 83.12 % Cbeta Deviations : 0.39 % 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: 2.94 (0.57), residues: 262 helix: 2.66 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -1.24 (1.05), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 144 HIS 0.002 0.000 HIS R 98 PHE 0.023 0.001 PHE R 75 TYR 0.020 0.002 TYR R 245 ARG 0.002 0.000 ARG R 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.242 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0988 time to fit residues: 4.5842 Evaluate side-chains 36 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.236 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 25 optimal weight: 0.0980 chunk 23 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 12 optimal weight: 0.1980 chunk 16 optimal weight: 0.0980 chunk 21 optimal weight: 0.2980 chunk 6 optimal weight: 0.7980 chunk 19 optimal weight: 0.0040 chunk 3 optimal weight: 0.0870 overall best weight: 0.0970 ------------------------------------------------------------------------------- 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: 0.7205 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 2196 Z= 0.127 Angle : 0.478 6.375 2969 Z= 0.243 Chirality : 0.034 0.127 351 Planarity : 0.004 0.047 348 Dihedral : 6.062 52.074 342 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.43 % Allowed : 17.32 % Favored : 82.25 % Cbeta Deviations : 0.39 % 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: 3.19 (0.56), residues: 262 helix: 2.95 (0.37), residues: 208 sheet: None (None), residues: 0 loop : -1.53 (0.97), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 144 HIS 0.001 0.000 HIS R 98 PHE 0.019 0.001 PHE R 75 TYR 0.019 0.002 TYR R 245 ARG 0.001 0.000 ARG R 262 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.226 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 37 average time/residue: 0.0989 time to fit residues: 4.7102 Evaluate side-chains 36 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.228 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 14 optimal weight: 0.0000 chunk 23 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.5584 ------------------------------------------------------------------------------- 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: 0.7262 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2196 Z= 0.159 Angle : 0.519 6.936 2969 Z= 0.260 Chirality : 0.036 0.142 351 Planarity : 0.004 0.046 348 Dihedral : 6.364 56.920 342 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 17.32 % Favored : 82.68 % Cbeta Deviations : 0.39 % 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: 3.27 (0.56), residues: 262 helix: 2.90 (0.37), residues: 211 sheet: None (None), residues: 0 loop : -1.24 (1.03), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 144 HIS 0.001 0.000 HIS R 98 PHE 0.024 0.001 PHE R 75 TYR 0.020 0.002 TYR R 245 ARG 0.002 0.000 ARG R 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.224 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0979 time to fit residues: 4.3988 Evaluate side-chains 33 residues out of total 242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.225 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 3 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3881 r_free = 0.3881 target = 0.163652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.138288 restraints weight = 2460.493| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.74 r_work: 0.3382 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2196 Z= 0.184 Angle : 0.546 6.992 2969 Z= 0.278 Chirality : 0.037 0.149 351 Planarity : 0.005 0.046 348 Dihedral : 6.684 58.092 342 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.87 % Allowed : 17.75 % Favored : 81.39 % Cbeta Deviations : 0.39 % 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: 3.17 (0.57), residues: 262 helix: 2.82 (0.37), residues: 211 sheet: None (None), residues: 0 loop : -1.26 (1.04), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 144 HIS 0.002 0.001 HIS R 98 PHE 0.029 0.002 PHE R 75 TYR 0.020 0.002 TYR R 245 ARG 0.002 0.000 ARG R 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1035.26 seconds wall clock time: 19 minutes 22.15 seconds (1162.15 seconds total)