Starting phenix.real_space_refine on Sun Mar 10 14:40:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8s_37358/03_2024/8w8s_37358_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8s_37358/03_2024/8w8s_37358.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8s_37358/03_2024/8w8s_37358_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8s_37358/03_2024/8w8s_37358_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8s_37358/03_2024/8w8s_37358_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8s_37358/03_2024/8w8s_37358.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8s_37358/03_2024/8w8s_37358.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8s_37358/03_2024/8w8s_37358_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8s_37358/03_2024/8w8s_37358_updated.pdb" } resolution = 3.3 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 15 5.16 5 C 1524 2.51 5 N 363 2.21 5 O 357 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2265 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2223 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 13, 'TRANS': 267} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "R" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'U7D': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.84, per 1000 atoms: 0.81 Number of scatterers: 2265 At special positions: 0 Unit cell: (56.95, 69.7, 71.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 F 6 9.00 O 357 8.00 N 363 7.00 C 1524 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 104 " - pdb=" SG CYS R 182 " distance=2.04 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: 0.98 Conformation dependent library (CDL) restraints added in 422.1 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: 544 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 9 helices and 0 sheets defined 74.0% 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 28 through 57 removed outlier: 3.717A pdb=" N VAL R 39 " --> pdb=" O SER R 35 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE R 40 " --> pdb=" O THR R 36 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE R 41 " --> pdb=" O VAL R 37 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU R 42 " --> pdb=" O LEU R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 92 Proline residue: R 86 - end of helix removed outlier: 4.249A pdb=" N SER R 92 " --> pdb=" O VAL R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 133 Processing helix chain 'R' and resid 145 through 161 Processing helix chain 'R' and resid 190 through 200 Processing helix chain 'R' and resid 202 through 227 removed outlier: 4.060A pdb=" N VAL R 214 " --> pdb=" O ALA R 210 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL R 215 " --> pdb=" O CYS R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 396 through 424 removed outlier: 4.199A pdb=" N VAL R 400 " --> pdb=" O LYS R 396 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE R 401 " --> pdb=" O ALA R 397 " (cutoff:3.500A) Proline residue: R 414 - end of helix removed outlier: 3.904A pdb=" N VAL R 423 " --> pdb=" O ALA R 419 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TRP R 424 " --> pdb=" O VAL R 420 " (cutoff:3.500A) Processing helix chain 'R' and resid 433 through 454 removed outlier: 3.798A pdb=" N PHE R 444 " --> pdb=" O ILE R 440 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU R 445 " --> pdb=" O TRP R 441 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLN R 446 " --> pdb=" O LEU R 442 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N CYS R 447 " --> pdb=" O PHE R 443 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N CYS R 448 " --> pdb=" O PHE R 444 " (cutoff:3.500A) Proline residue: R 451 - end of helix Processing helix chain 'R' and resid 459 through 472 147 hydrogen bonds defined for protein. 441 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: 0.55 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 635 1.34 - 1.46: 462 1.46 - 1.58: 1214 1.58 - 1.70: 2 1.70 - 1.82: 18 Bond restraints: 2331 Sorted by residual: bond pdb=" N VAL R 65 " pdb=" CA VAL R 65 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.66e+00 bond pdb=" N ASN R 100 " pdb=" CA ASN R 100 " ideal model delta sigma weight residual 1.455 1.491 -0.035 1.18e-02 7.18e+03 8.91e+00 bond pdb=" N TRP R 97 " pdb=" CA TRP R 97 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.04e-02 9.25e+03 8.81e+00 bond pdb=" N ILE R 185 " pdb=" CA ILE R 185 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.78e+00 bond pdb=" N LEU R 95 " pdb=" CA LEU R 95 " ideal model delta sigma weight residual 1.455 1.489 -0.035 1.26e-02 6.30e+03 7.66e+00 ... (remaining 2326 not shown) Histogram of bond angle deviations from ideal: 100.48 - 107.24: 83 107.24 - 113.99: 1373 113.99 - 120.75: 1029 120.75 - 127.50: 676 127.50 - 134.26: 33 Bond angle restraints: 3194 Sorted by residual: angle pdb=" N ASN R 179 " pdb=" CA ASN R 179 " pdb=" C ASN R 179 " ideal model delta sigma weight residual 114.31 107.81 6.50 1.29e+00 6.01e-01 2.54e+01 angle pdb=" C LEU R 63 " pdb=" CA LEU R 63 " pdb=" CB LEU R 63 " ideal model delta sigma weight residual 116.63 111.88 4.75 1.16e+00 7.43e-01 1.68e+01 angle pdb=" CA GLN R 61 " pdb=" C GLN R 61 " pdb=" O GLN R 61 " ideal model delta sigma weight residual 122.64 118.33 4.31 1.25e+00 6.40e-01 1.19e+01 angle pdb=" CA CYS R 182 " pdb=" C CYS R 182 " pdb=" O CYS R 182 " ideal model delta sigma weight residual 121.84 118.09 3.75 1.16e+00 7.43e-01 1.04e+01 angle pdb=" CA PHE R 96 " pdb=" C PHE R 96 " pdb=" O PHE R 96 " ideal model delta sigma weight residual 121.84 118.13 3.71 1.16e+00 7.43e-01 1.02e+01 ... (remaining 3189 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.80: 1110 16.80 - 33.60: 171 33.60 - 50.40: 41 50.40 - 67.20: 5 67.20 - 84.01: 1 Dihedral angle restraints: 1328 sinusoidal: 492 harmonic: 836 Sorted by residual: dihedral pdb=" CB CYS R 104 " pdb=" SG CYS R 104 " pdb=" SG CYS R 182 " pdb=" CB CYS R 182 " ideal model delta sinusoidal sigma weight residual -86.00 -20.68 -65.32 1 1.00e+01 1.00e-02 5.59e+01 dihedral pdb=" CA THR R 164 " pdb=" C THR R 164 " pdb=" N PRO R 165 " pdb=" CA PRO R 165 " ideal model delta harmonic sigma weight residual 180.00 156.45 23.55 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" C PHE R 96 " pdb=" N PHE R 96 " pdb=" CA PHE R 96 " pdb=" CB PHE R 96 " ideal model delta harmonic sigma weight residual -122.60 -131.31 8.71 0 2.50e+00 1.60e-01 1.21e+01 ... (remaining 1325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 278 0.045 - 0.090: 77 0.090 - 0.136: 21 0.136 - 0.181: 6 0.181 - 0.226: 1 Chirality restraints: 383 Sorted by residual: chirality pdb=" CA PHE R 96 " pdb=" N PHE R 96 " pdb=" C PHE R 96 " pdb=" CB PHE R 96 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB VAL R 65 " pdb=" CA VAL R 65 " pdb=" CG1 VAL R 65 " pdb=" CG2 VAL R 65 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.41e-01 chirality pdb=" CA MET R 184 " pdb=" N MET R 184 " pdb=" C MET R 184 " pdb=" CB MET R 184 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.85e-01 ... (remaining 380 not shown) Planarity restraints: 375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR R 164 " -0.058 5.00e-02 4.00e+02 8.76e-02 1.23e+01 pdb=" N PRO R 165 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO R 165 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO R 165 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 413 " -0.023 5.00e-02 4.00e+02 3.46e-02 1.91e+00 pdb=" N PRO R 414 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO R 414 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO R 414 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO R 165 " 0.022 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO R 166 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO R 166 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 166 " 0.018 5.00e-02 4.00e+02 ... (remaining 372 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 697 2.83 - 3.35: 2248 3.35 - 3.86: 3532 3.86 - 4.38: 3432 4.38 - 4.90: 6441 Nonbonded interactions: 16350 Sorted by model distance: nonbonded pdb=" O THR R 164 " pdb=" OG1 THR R 164 " model vdw 2.310 2.440 nonbonded pdb=" OD1 ASP R 176 " pdb=" N LEU R 181 " model vdw 2.446 2.520 nonbonded pdb=" O SER R 45 " pdb=" ND2 ASN R 49 " model vdw 2.448 2.520 nonbonded pdb=" O LEU R 62 " pdb=" ND2 ASN R 67 " model vdw 2.478 2.520 nonbonded pdb=" OD1 ASN R 72 " pdb=" OG1 THR R 121 " model vdw 2.510 2.440 ... (remaining 16345 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.240 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: 1.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.090 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 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 : 0.005 0.039 2331 Z= 0.304 Angle : 0.773 6.673 3194 Z= 0.497 Chirality : 0.047 0.226 383 Planarity : 0.006 0.088 375 Dihedral : 16.340 84.006 781 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.64 % Allowed : 22.95 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.52), residues: 277 helix: 2.25 (0.36), residues: 202 sheet: None (None), residues: 0 loop : -2.60 (0.68), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 441 HIS 0.001 0.000 HIS R 135 PHE 0.011 0.001 PHE R 200 TYR 0.009 0.001 TYR R 454 ARG 0.003 0.000 ARG R 178 *********************** 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 32 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.345 Fit side-chains REVERT: R 79 LEU cc_start: 0.7987 (mp) cc_final: 0.7670 (mp) REVERT: R 97 TRP cc_start: 0.8799 (t-100) cc_final: 0.8335 (m-90) REVERT: R 457 MET cc_start: 0.8773 (mtp) cc_final: 0.8542 (mtp) outliers start: 4 outliers final: 1 residues processed: 32 average time/residue: 0.1569 time to fit residues: 6.0412 Evaluate side-chains 28 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 27 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 99 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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: 0.7884 moved from start: 0.0654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2331 Z= 0.181 Angle : 0.528 5.764 3194 Z= 0.271 Chirality : 0.041 0.168 383 Planarity : 0.006 0.076 375 Dihedral : 6.066 44.859 305 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.28 % Allowed : 22.13 % Favored : 74.59 % 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: 2.04 (0.52), residues: 277 helix: 2.67 (0.35), residues: 202 sheet: None (None), residues: 0 loop : -2.64 (0.68), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 441 HIS 0.001 0.000 HIS R 135 PHE 0.014 0.001 PHE R 103 TYR 0.009 0.001 TYR R 454 ARG 0.003 0.000 ARG R 221 *********************** 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 38 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 30 time to evaluate : 0.406 Fit side-chains REVERT: R 59 LYS cc_start: 0.8472 (mttp) cc_final: 0.8260 (mttt) REVERT: R 97 TRP cc_start: 0.8805 (t-100) cc_final: 0.8380 (t-100) REVERT: R 457 MET cc_start: 0.8829 (mtp) cc_final: 0.8603 (mtp) REVERT: R 464 GLU cc_start: 0.8753 (tp30) cc_final: 0.8550 (tp30) outliers start: 8 outliers final: 6 residues processed: 35 average time/residue: 0.1406 time to fit residues: 5.9937 Evaluate side-chains 32 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 26 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 200 PHE Chi-restraints excluded: chain R residue 468 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 12 optimal weight: 0.0980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7879 moved from start: 0.0813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 2331 Z= 0.159 Angle : 0.514 5.736 3194 Z= 0.258 Chirality : 0.041 0.163 383 Planarity : 0.005 0.073 375 Dihedral : 4.934 42.566 303 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.51 % Allowed : 21.72 % Favored : 73.77 % 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 (0.52), residues: 277 helix: 2.79 (0.35), residues: 202 sheet: None (None), residues: 0 loop : -2.62 (0.67), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 441 HIS 0.001 0.000 HIS R 135 PHE 0.012 0.001 PHE R 96 TYR 0.009 0.001 TYR R 454 ARG 0.003 0.000 ARG R 221 *********************** 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 40 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 29 time to evaluate : 0.253 Fit side-chains REVERT: R 59 LYS cc_start: 0.8517 (mttp) cc_final: 0.8269 (mttt) REVERT: R 457 MET cc_start: 0.8814 (mtp) cc_final: 0.8584 (mtp) REVERT: R 464 GLU cc_start: 0.8774 (tp30) cc_final: 0.8559 (tp30) outliers start: 11 outliers final: 5 residues processed: 37 average time/residue: 0.1258 time to fit residues: 5.7152 Evaluate side-chains 33 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 28 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 SER Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 200 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 15 optimal weight: 0.0170 chunk 0 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 0.0670 chunk 23 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- 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: 0.7893 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2331 Z= 0.167 Angle : 0.529 8.401 3194 Z= 0.259 Chirality : 0.040 0.160 383 Planarity : 0.005 0.068 375 Dihedral : 4.779 39.947 303 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.05 % Allowed : 24.18 % Favored : 73.77 % 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: 2.36 (0.52), residues: 277 helix: 2.93 (0.35), residues: 202 sheet: None (None), residues: 0 loop : -2.61 (0.66), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 441 HIS 0.001 0.000 HIS R 135 PHE 0.010 0.001 PHE R 96 TYR 0.008 0.001 TYR R 454 ARG 0.002 0.000 ARG R 221 *********************** 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 34 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 29 time to evaluate : 0.276 Fit side-chains REVERT: R 59 LYS cc_start: 0.8537 (mttp) cc_final: 0.8253 (mttt) REVERT: R 457 MET cc_start: 0.8817 (mtp) cc_final: 0.8574 (mtp) REVERT: R 464 GLU cc_start: 0.8796 (tp30) cc_final: 0.8545 (tp30) outliers start: 5 outliers final: 5 residues processed: 33 average time/residue: 0.1526 time to fit residues: 6.1035 Evaluate side-chains 32 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 27 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 200 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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: 0.7901 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2331 Z= 0.170 Angle : 0.530 9.235 3194 Z= 0.258 Chirality : 0.040 0.158 383 Planarity : 0.005 0.066 375 Dihedral : 4.649 39.315 303 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.28 % Allowed : 24.59 % Favored : 72.13 % 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: 2.39 (0.53), residues: 277 helix: 2.98 (0.35), residues: 203 sheet: None (None), residues: 0 loop : -2.77 (0.65), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 441 HIS 0.001 0.000 HIS R 135 PHE 0.008 0.001 PHE R 200 TYR 0.008 0.001 TYR R 454 ARG 0.001 0.000 ARG R 221 *********************** 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 37 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 29 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: R 59 LYS cc_start: 0.8552 (mttp) cc_final: 0.8290 (mttt) REVERT: R 457 MET cc_start: 0.8805 (mtp) cc_final: 0.8551 (mtp) outliers start: 8 outliers final: 4 residues processed: 36 average time/residue: 0.1322 time to fit residues: 5.8521 Evaluate side-chains 33 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 SER Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 200 PHE Chi-restraints excluded: chain R residue 468 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7899 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2331 Z= 0.166 Angle : 0.517 6.851 3194 Z= 0.256 Chirality : 0.040 0.158 383 Planarity : 0.005 0.067 375 Dihedral : 4.558 38.846 303 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.87 % Allowed : 25.82 % Favored : 71.31 % 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: 2.41 (0.53), residues: 277 helix: 2.99 (0.35), residues: 203 sheet: None (None), residues: 0 loop : -2.75 (0.65), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 170 HIS 0.001 0.000 HIS R 135 PHE 0.008 0.001 PHE R 200 TYR 0.009 0.001 TYR R 454 ARG 0.001 0.000 ARG R 221 *********************** 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 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 30 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: R 59 LYS cc_start: 0.8580 (mttp) cc_final: 0.8310 (mttt) REVERT: R 457 MET cc_start: 0.8806 (mtp) cc_final: 0.8551 (mtp) outliers start: 7 outliers final: 4 residues processed: 36 average time/residue: 0.1381 time to fit residues: 6.0821 Evaluate side-chains 32 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 SER Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 200 PHE Chi-restraints excluded: chain R residue 468 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 15 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 430 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2331 Z= 0.243 Angle : 0.557 6.329 3194 Z= 0.280 Chirality : 0.041 0.149 383 Planarity : 0.005 0.069 375 Dihedral : 4.645 39.961 303 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.28 % Allowed : 25.82 % Favored : 70.90 % 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 (0.53), residues: 277 helix: 2.95 (0.36), residues: 203 sheet: None (None), residues: 0 loop : -2.82 (0.64), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 170 HIS 0.002 0.001 HIS R 135 PHE 0.008 0.001 PHE R 200 TYR 0.009 0.001 TYR R 454 ARG 0.001 0.000 ARG R 178 *********************** 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 36 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 28 time to evaluate : 0.267 Fit side-chains REVERT: R 178 ARG cc_start: 0.9252 (tpt90) cc_final: 0.8967 (ttt-90) REVERT: R 457 MET cc_start: 0.8779 (mtp) cc_final: 0.8475 (mtp) outliers start: 8 outliers final: 6 residues processed: 35 average time/residue: 0.1370 time to fit residues: 5.9111 Evaluate side-chains 32 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 26 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 SER Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 200 PHE Chi-restraints excluded: chain R residue 403 ILE Chi-restraints excluded: chain R residue 468 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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: 0.7945 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2331 Z= 0.199 Angle : 0.560 7.975 3194 Z= 0.272 Chirality : 0.041 0.157 383 Planarity : 0.005 0.069 375 Dihedral : 4.626 40.741 303 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.87 % Allowed : 26.64 % Favored : 70.49 % 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: 2.37 (0.52), residues: 277 helix: 2.97 (0.35), residues: 203 sheet: None (None), residues: 0 loop : -2.80 (0.63), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 170 HIS 0.001 0.000 HIS R 135 PHE 0.009 0.001 PHE R 200 TYR 0.009 0.001 TYR R 454 ARG 0.001 0.000 ARG R 221 *********************** 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 35 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 28 time to evaluate : 0.284 Fit side-chains REVERT: R 178 ARG cc_start: 0.9228 (tpt90) cc_final: 0.8908 (ttt-90) REVERT: R 457 MET cc_start: 0.8774 (mtp) cc_final: 0.8494 (mtp) outliers start: 7 outliers final: 4 residues processed: 33 average time/residue: 0.1413 time to fit residues: 5.6994 Evaluate side-chains 31 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 27 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 SER Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 468 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 0.7980 chunk 23 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 20 optimal weight: 0.2980 chunk 3 optimal weight: 0.0270 chunk 22 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 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: 0.7903 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2331 Z= 0.163 Angle : 0.555 7.668 3194 Z= 0.267 Chirality : 0.040 0.160 383 Planarity : 0.005 0.068 375 Dihedral : 4.547 39.988 303 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.05 % Allowed : 27.87 % Favored : 70.08 % 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: 2.43 (0.52), residues: 277 helix: 3.01 (0.35), residues: 202 sheet: None (None), residues: 0 loop : -2.68 (0.63), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 441 HIS 0.001 0.000 HIS R 135 PHE 0.009 0.001 PHE R 200 TYR 0.009 0.001 TYR R 454 ARG 0.003 0.000 ARG R 58 *********************** 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 34 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 29 time to evaluate : 0.276 Fit side-chains REVERT: R 178 ARG cc_start: 0.9193 (tpt90) cc_final: 0.8920 (ttt-90) outliers start: 5 outliers final: 4 residues processed: 33 average time/residue: 0.1541 time to fit residues: 6.2306 Evaluate side-chains 32 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 SER Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 200 PHE Chi-restraints excluded: chain R residue 468 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 0.0770 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.7338 ------------------------------------------------------------------------------- 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: 0.7903 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2331 Z= 0.166 Angle : 0.550 7.287 3194 Z= 0.265 Chirality : 0.040 0.159 383 Planarity : 0.005 0.067 375 Dihedral : 4.407 39.142 303 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.23 % Allowed : 27.87 % Favored : 70.90 % 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: 2.51 (0.53), residues: 277 helix: 3.07 (0.35), residues: 203 sheet: None (None), residues: 0 loop : -2.73 (0.65), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 441 HIS 0.002 0.000 HIS R 135 PHE 0.010 0.001 PHE R 200 TYR 0.010 0.001 TYR R 454 ARG 0.001 0.000 ARG R 221 ********************** 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 33 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 30 time to evaluate : 0.289 Fit side-chains REVERT: R 178 ARG cc_start: 0.9210 (tpt90) cc_final: 0.8945 (ttt-90) outliers start: 3 outliers final: 3 residues processed: 32 average time/residue: 0.1285 time to fit residues: 5.0554 Evaluate side-chains 31 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 28 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 SER Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 468 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 3 optimal weight: 0.1980 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 0.0060 chunk 2 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 = 0.3431 r_free = 0.3431 target = 0.092577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.076464 restraints weight = 5113.730| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.84 r_work: 0.3058 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 2331 Z= 0.157 Angle : 0.548 7.354 3194 Z= 0.263 Chirality : 0.040 0.160 383 Planarity : 0.005 0.066 375 Dihedral : 4.352 38.685 303 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.64 % Allowed : 27.05 % Favored : 71.31 % 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: 2.56 (0.53), residues: 277 helix: 3.11 (0.35), residues: 203 sheet: None (None), residues: 0 loop : -2.71 (0.66), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 441 HIS 0.001 0.000 HIS R 135 PHE 0.010 0.001 PHE R 200 TYR 0.009 0.001 TYR R 454 ARG 0.001 0.000 ARG R 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 900.91 seconds wall clock time: 17 minutes 25.50 seconds (1045.50 seconds total)