Starting phenix.real_space_refine on Wed Nov 13 23:16:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggy_40025/11_2024/8ggy_40025.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggy_40025/11_2024/8ggy_40025.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggy_40025/11_2024/8ggy_40025.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggy_40025/11_2024/8ggy_40025.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggy_40025/11_2024/8ggy_40025.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggy_40025/11_2024/8ggy_40025.cif" } resolution = 3.9 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= 0.018 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 13 5.16 5 C 1388 2.51 5 N 339 2.21 5 O 356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 2096 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2081 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'ASP:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 2, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 73 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.48, per 1000 atoms: 1.18 Number of scatterers: 2096 At special positions: 0 Unit cell: (54.6651, 85.9023, 62.4744, 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 13 16.00 O 356 8.00 N 339 7.00 C 1388 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 280.4 milliseconds 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 538 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 85.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'R' and resid 32 through 61 removed outlier: 3.619A pdb=" N MET R 36 " --> pdb=" O TRP R 32 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 86 Processing helix chain 'R' and resid 86 through 96 Processing helix chain 'R' and resid 103 through 137 removed outlier: 4.335A pdb=" N GLU R 107 " --> pdb=" O ASN R 103 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG R 131 " --> pdb=" O ILE R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 164 removed outlier: 3.690A pdb=" N ALA R 150 " --> pdb=" O THR R 146 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 171 removed outlier: 3.760A pdb=" N MET R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 187 Processing helix chain 'R' and resid 196 through 208 removed outlier: 3.719A pdb=" N ALA R 200 " --> pdb=" O ASN R 196 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE R 201 " --> pdb=" O GLN R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 237 Processing helix chain 'R' and resid 270 through 299 removed outlier: 3.788A pdb=" N THR R 274 " --> pdb=" O LYS R 270 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.774A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 316 Processing helix chain 'R' and resid 317 through 327 removed outlier: 3.584A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 340 removed outlier: 3.513A pdb=" N LEU R 340 " --> pdb=" O PHE R 336 " (cutoff:3.500A) 160 hydrogen bonds defined for protein. 480 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: 0.50 Time building geometry restraints manager: 0.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 643 1.34 - 1.46: 589 1.46 - 1.58: 900 1.58 - 1.70: 0 1.70 - 1.82: 19 Bond restraints: 2151 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.453 -0.056 2.00e-02 2.50e+03 7.78e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.578 -0.055 2.00e-02 2.50e+03 7.56e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.443 -0.049 2.00e-02 2.50e+03 6.08e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.567 -0.047 2.00e-02 2.50e+03 5.51e+00 bond pdb=" CAI G1I R 501 " pdb=" NAN G1I R 501 " ideal model delta sigma weight residual 1.451 1.497 -0.046 2.00e-02 2.50e+03 5.21e+00 ... (remaining 2146 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 2843 1.38 - 2.75: 77 2.75 - 4.13: 19 4.13 - 5.51: 10 5.51 - 6.88: 2 Bond angle restraints: 2951 Sorted by residual: angle pdb=" C GLU R 180 " pdb=" N ALA R 181 " pdb=" CA ALA R 181 " ideal model delta sigma weight residual 121.54 128.17 -6.63 1.91e+00 2.74e-01 1.21e+01 angle pdb=" C VAL R 295 " pdb=" N HIS R 296 " pdb=" CA HIS R 296 " ideal model delta sigma weight residual 120.72 116.07 4.65 1.67e+00 3.59e-01 7.75e+00 angle pdb=" CB MET R 279 " pdb=" CG MET R 279 " pdb=" SD MET R 279 " ideal model delta sigma weight residual 112.70 119.58 -6.88 3.00e+00 1.11e-01 5.26e+00 angle pdb=" CA GLN R 337 " pdb=" CB GLN R 337 " pdb=" CG GLN R 337 " ideal model delta sigma weight residual 114.10 118.62 -4.52 2.00e+00 2.50e-01 5.10e+00 angle pdb=" C ASP R 300 " pdb=" N ASN R 301 " pdb=" CA ASN R 301 " ideal model delta sigma weight residual 123.05 126.33 -3.28 1.57e+00 4.06e-01 4.36e+00 ... (remaining 2946 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.70: 1088 15.70 - 31.39: 95 31.39 - 47.09: 32 47.09 - 62.78: 5 62.78 - 78.48: 4 Dihedral angle restraints: 1224 sinusoidal: 396 harmonic: 828 Sorted by residual: dihedral pdb=" CA PHE R 208 " pdb=" C PHE R 208 " pdb=" N TYR R 209 " pdb=" CA TYR R 209 " ideal model delta harmonic sigma weight residual 180.00 -164.67 -15.33 0 5.00e+00 4.00e-02 9.40e+00 dihedral pdb=" CA ARG R 131 " pdb=" CB ARG R 131 " pdb=" CG ARG R 131 " pdb=" CD ARG R 131 " ideal model delta sinusoidal sigma weight residual -180.00 -126.96 -53.04 3 1.50e+01 4.44e-03 9.17e+00 dihedral pdb=" CA ILE R 325 " pdb=" C ILE R 325 " pdb=" N TYR R 326 " pdb=" CA TYR R 326 " ideal model delta harmonic sigma weight residual 180.00 -165.11 -14.89 0 5.00e+00 4.00e-02 8.87e+00 ... (remaining 1221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 237 0.035 - 0.069: 91 0.069 - 0.103: 22 0.103 - 0.138: 3 0.138 - 0.172: 1 Chirality restraints: 354 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.57 -0.17 2.00e-01 2.50e+01 7.43e-01 chirality pdb=" CA ILE R 303 " pdb=" N ILE R 303 " pdb=" C ILE R 303 " pdb=" CB ILE R 303 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CB VAL R 295 " pdb=" CA VAL R 295 " pdb=" CG1 VAL R 295 " pdb=" CG2 VAL R 295 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.18e-01 ... (remaining 351 not shown) Planarity restraints: 363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER R 329 " -0.029 5.00e-02 4.00e+02 4.39e-02 3.08e+00 pdb=" N PRO R 330 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO R 330 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 330 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 198 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.31e+00 pdb=" C ALA R 198 " 0.020 2.00e-02 2.50e+03 pdb=" O ALA R 198 " -0.007 2.00e-02 2.50e+03 pdb=" N TYR R 199 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR R 281 " -0.004 2.00e-02 2.50e+03 8.53e-03 7.27e-01 pdb=" C THR R 281 " 0.015 2.00e-02 2.50e+03 pdb=" O THR R 281 " -0.006 2.00e-02 2.50e+03 pdb=" N PHE R 282 " -0.005 2.00e-02 2.50e+03 ... (remaining 360 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 784 2.88 - 3.39: 2232 3.39 - 3.89: 3300 3.89 - 4.40: 3172 4.40 - 4.90: 5820 Nonbonded interactions: 15308 Sorted by model distance: nonbonded pdb=" O ALA R 92 " pdb=" OG1 THR R 96 " model vdw 2.377 3.040 nonbonded pdb=" O TRP R 99 " pdb=" OG1 THR R 100 " model vdw 2.438 3.040 nonbonded pdb=" OD1 ASP R 130 " pdb=" N ARG R 131 " model vdw 2.481 3.120 nonbonded pdb=" O GLN R 337 " pdb=" OE1 GLN R 337 " model vdw 2.559 3.040 nonbonded pdb=" O ILE R 127 " pdb=" OD1 ASP R 130 " model vdw 2.585 3.040 ... (remaining 15303 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.280 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 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 0.056 2151 Z= 0.242 Angle : 0.631 6.883 2951 Z= 0.330 Chirality : 0.040 0.172 354 Planarity : 0.004 0.044 363 Dihedral : 14.743 78.477 686 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % 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: 2.19 (0.51), residues: 277 helix: 2.21 (0.36), residues: 217 sheet: None (None), residues: 0 loop : -1.51 (0.67), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 109 HIS 0.002 0.001 HIS R 296 PHE 0.009 0.001 PHE R 290 TYR 0.006 0.001 TYR R 326 ARG 0.003 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.299 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1288 time to fit residues: 6.9465 Evaluate side-chains 32 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 0.0370 chunk 25 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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: 0.7966 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2151 Z= 0.178 Angle : 0.558 5.821 2951 Z= 0.298 Chirality : 0.040 0.131 354 Planarity : 0.004 0.042 363 Dihedral : 3.928 15.373 312 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.63 % Allowed : 10.88 % Favored : 85.49 % 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: 2.17 (0.51), residues: 277 helix: 2.04 (0.35), residues: 224 sheet: None (None), residues: 0 loop : -1.23 (0.70), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 109 HIS 0.001 0.001 HIS R 296 PHE 0.017 0.001 PHE R 104 TYR 0.018 0.001 TYR R 308 ARG 0.004 0.001 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.285 Fit side-chains REVERT: R 339 LEU cc_start: 0.8504 (mm) cc_final: 0.8205 (mm) outliers start: 7 outliers final: 5 residues processed: 40 average time/residue: 0.1335 time to fit residues: 6.4359 Evaluate side-chains 36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 19 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7982 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2151 Z= 0.178 Angle : 0.545 5.182 2951 Z= 0.295 Chirality : 0.040 0.136 354 Planarity : 0.004 0.040 363 Dihedral : 3.960 15.318 312 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 5.18 % Allowed : 14.51 % Favored : 80.31 % 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: 2.12 (0.51), residues: 277 helix: 2.03 (0.35), residues: 224 sheet: None (None), residues: 0 loop : -1.38 (0.70), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 109 HIS 0.001 0.001 HIS R 296 PHE 0.018 0.001 PHE R 104 TYR 0.013 0.001 TYR R 308 ARG 0.003 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.265 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 39 average time/residue: 0.1370 time to fit residues: 6.4557 Evaluate side-chains 36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 324 LEU Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 13 optimal weight: 0.0270 chunk 24 optimal weight: 0.6980 chunk 6 optimal weight: 0.0980 overall best weight: 0.4438 ------------------------------------------------------------------------------- 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: 0.7967 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2151 Z= 0.156 Angle : 0.532 6.446 2951 Z= 0.285 Chirality : 0.039 0.131 354 Planarity : 0.004 0.040 363 Dihedral : 3.886 15.322 312 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.66 % Allowed : 15.54 % Favored : 79.79 % 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: 2.25 (0.51), residues: 277 helix: 2.08 (0.35), residues: 226 sheet: None (None), residues: 0 loop : -1.23 (0.72), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 109 HIS 0.001 0.000 HIS R 296 PHE 0.017 0.001 PHE R 104 TYR 0.012 0.001 TYR R 308 ARG 0.004 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.240 Fit side-chains REVERT: R 40 MET cc_start: 0.7373 (mtt) cc_final: 0.7021 (mtt) outliers start: 9 outliers final: 7 residues processed: 35 average time/residue: 0.1357 time to fit residues: 5.7449 Evaluate side-chains 35 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 0.9990 chunk 24 optimal weight: 0.0040 chunk 5 optimal weight: 0.5980 chunk 15 optimal weight: 0.2980 chunk 6 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 14 optimal weight: 0.0070 overall best weight: 0.3210 ------------------------------------------------------------------------------- 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: 0.7933 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 2151 Z= 0.142 Angle : 0.540 5.682 2951 Z= 0.284 Chirality : 0.040 0.133 354 Planarity : 0.004 0.039 363 Dihedral : 3.781 15.412 312 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.66 % Allowed : 18.65 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.51), residues: 277 helix: 2.19 (0.35), residues: 226 sheet: None (None), residues: 0 loop : -1.28 (0.71), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.001 0.000 HIS R 296 PHE 0.014 0.001 PHE R 104 TYR 0.010 0.001 TYR R 308 ARG 0.004 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.245 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 34 average time/residue: 0.1354 time to fit residues: 5.5624 Evaluate side-chains 37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 279 MET Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 324 LEU Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 5 optimal weight: 0.0270 chunk 17 optimal weight: 0.6980 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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: 0.7980 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2151 Z= 0.172 Angle : 0.563 6.725 2951 Z= 0.295 Chirality : 0.040 0.132 354 Planarity : 0.004 0.039 363 Dihedral : 3.841 15.549 312 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 5.18 % Allowed : 18.65 % Favored : 76.17 % 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: 2.33 (0.50), residues: 277 helix: 2.14 (0.35), residues: 226 sheet: None (None), residues: 0 loop : -1.26 (0.72), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.001 0.000 HIS R 296 PHE 0.013 0.001 PHE R 104 TYR 0.012 0.001 TYR R 308 ARG 0.004 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 27 time to evaluate : 0.185 Fit side-chains REVERT: R 339 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8099 (mm) outliers start: 10 outliers final: 7 residues processed: 32 average time/residue: 0.1456 time to fit residues: 5.5458 Evaluate side-chains 36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 279 MET Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 2 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 24 optimal weight: 0.0050 chunk 25 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 7 optimal weight: 0.3980 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: 0.7958 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 2151 Z= 0.154 Angle : 0.555 6.474 2951 Z= 0.289 Chirality : 0.040 0.131 354 Planarity : 0.004 0.039 363 Dihedral : 3.784 15.469 312 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 5.70 % Allowed : 19.17 % Favored : 75.13 % 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: 2.42 (0.51), residues: 277 helix: 2.21 (0.35), residues: 226 sheet: None (None), residues: 0 loop : -1.25 (0.72), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 109 HIS 0.001 0.000 HIS R 296 PHE 0.012 0.001 PHE R 104 TYR 0.011 0.001 TYR R 308 ARG 0.004 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 28 time to evaluate : 0.265 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 34 average time/residue: 0.1486 time to fit residues: 6.0621 Evaluate side-chains 34 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 279 MET Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 12 optimal weight: 0.3980 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 17 optimal weight: 0.2980 chunk 13 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.7989 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2151 Z= 0.174 Angle : 0.564 6.689 2951 Z= 0.296 Chirality : 0.040 0.130 354 Planarity : 0.004 0.039 363 Dihedral : 3.846 15.551 312 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.66 % Allowed : 19.17 % Favored : 76.17 % 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: 2.34 (0.50), residues: 277 helix: 2.18 (0.35), residues: 225 sheet: None (None), residues: 0 loop : -1.37 (0.73), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.001 0.001 HIS R 296 PHE 0.011 0.001 PHE R 104 TYR 0.012 0.001 TYR R 308 ARG 0.004 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.296 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 33 average time/residue: 0.1527 time to fit residues: 6.1036 Evaluate side-chains 34 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 279 MET Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.8020 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2151 Z= 0.195 Angle : 0.588 7.038 2951 Z= 0.309 Chirality : 0.040 0.130 354 Planarity : 0.004 0.038 363 Dihedral : 3.952 15.583 312 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.15 % Allowed : 19.69 % Favored : 76.17 % 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: 2.23 (0.50), residues: 277 helix: 2.14 (0.35), residues: 223 sheet: None (None), residues: 0 loop : -1.42 (0.69), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.001 0.001 HIS R 296 PHE 0.011 0.001 PHE R 104 TYR 0.013 0.001 TYR R 308 ARG 0.004 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.254 Fit side-chains REVERT: R 339 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8218 (mm) outliers start: 8 outliers final: 7 residues processed: 34 average time/residue: 0.1515 time to fit residues: 6.2505 Evaluate side-chains 36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 279 MET Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.0970 chunk 27 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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: 0.7999 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2151 Z= 0.174 Angle : 0.581 7.194 2951 Z= 0.304 Chirality : 0.040 0.130 354 Planarity : 0.004 0.039 363 Dihedral : 3.903 15.608 312 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 5.18 % Allowed : 19.17 % Favored : 75.65 % 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: 2.28 (0.50), residues: 277 helix: 2.18 (0.35), residues: 223 sheet: None (None), residues: 0 loop : -1.43 (0.69), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.001 0.001 HIS R 296 PHE 0.011 0.001 PHE R 104 TYR 0.012 0.001 TYR R 308 ARG 0.004 0.000 ARG R 228 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.245 Fit side-chains REVERT: R 339 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8155 (mm) outliers start: 10 outliers final: 7 residues processed: 34 average time/residue: 0.1459 time to fit residues: 5.9637 Evaluate side-chains 36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 279 MET Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 3 optimal weight: 0.4980 chunk 5 optimal weight: 0.2980 chunk 22 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 18 optimal weight: 0.2980 chunk 9 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3437 r_free = 0.3437 target = 0.127006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.114162 restraints weight = 3778.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.116887 restraints weight = 2051.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.118806 restraints weight = 1280.779| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2151 Z= 0.179 Angle : 0.587 7.059 2951 Z= 0.309 Chirality : 0.040 0.130 354 Planarity : 0.004 0.039 363 Dihedral : 3.908 15.596 312 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.15 % Allowed : 20.21 % Favored : 75.65 % 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: 2.27 (0.50), residues: 277 helix: 2.13 (0.35), residues: 224 sheet: None (None), residues: 0 loop : -1.28 (0.76), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.001 0.001 HIS R 296 PHE 0.011 0.001 PHE R 104 TYR 0.012 0.001 TYR R 308 ARG 0.004 0.000 ARG R 228 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 953.66 seconds wall clock time: 22 minutes 47.93 seconds (1367.93 seconds total)