Starting phenix.real_space_refine on Mon Sep 23 13:23:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyk_21967/09_2024/6wyk_21967.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyk_21967/09_2024/6wyk_21967.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyk_21967/09_2024/6wyk_21967.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyk_21967/09_2024/6wyk_21967.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyk_21967/09_2024/6wyk_21967.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyk_21967/09_2024/6wyk_21967.cif" } resolution = 4.0 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= 0.003 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 18 5.16 5 C 2029 2.51 5 N 490 2.21 5 O 546 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3083 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3083 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 396} Chain breaks: 1 Time building chain proxies: 2.70, per 1000 atoms: 0.88 Number of scatterers: 3083 At special positions: 0 Unit cell: (73.95, 70.992, 76.908, 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 18 16.00 O 546 8.00 N 490 7.00 C 2029 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: 0.86 Conformation dependent library (CDL) restraints added in 384.5 milliseconds 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 750 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 86.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 5 through 10 Processing helix chain 'A' and resid 13 through 29 removed outlier: 4.045A pdb=" N LEU A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 78 Proline residue: A 45 - end of helix removed outlier: 3.508A pdb=" N PHE A 50 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N MET A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Proline residue: A 60 - end of helix removed outlier: 3.530A pdb=" N PHE A 63 " --> pdb=" O MET A 59 " (cutoff:3.500A) Proline residue: A 75 - end of helix Processing helix chain 'A' and resid 79 through 108 Processing helix chain 'A' and resid 129 through 137 removed outlier: 3.510A pdb=" N ILE A 133 " --> pdb=" O PRO A 129 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 149 removed outlier: 3.671A pdb=" N GLY A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 170 removed outlier: 4.268A pdb=" N ASN A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 221 removed outlier: 4.025A pdb=" N GLN A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 206 - end of helix removed outlier: 3.780A pdb=" N GLN A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 255 removed outlier: 3.832A pdb=" N GLU A 227 " --> pdb=" O LYS A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 276 removed outlier: 4.420A pdb=" N ASP A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 293 removed outlier: 4.021A pdb=" N VAL A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 Proline residue: A 304 - end of helix Processing helix chain 'A' and resid 312 through 330 Processing helix chain 'A' and resid 334 through 352 Processing helix chain 'A' and resid 357 through 370 removed outlier: 4.388A pdb=" N ILE A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET A 365 " --> pdb=" O ILE A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 416 removed outlier: 3.667A pdb=" N GLY A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE A 389 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET A 399 " --> pdb=" O MET A 395 " (cutoff:3.500A) 251 hydrogen bonds defined for protein. 753 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: 0.91 Time building geometry restraints manager: 1.00 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: 946 1.34 - 1.46: 451 1.46 - 1.57: 1705 1.57 - 1.69: 0 1.69 - 1.81: 34 Bond restraints: 3136 Sorted by residual: bond pdb=" N VAL A 225 " pdb=" CA VAL A 225 " ideal model delta sigma weight residual 1.459 1.507 -0.048 1.33e-02 5.65e+03 1.29e+01 bond pdb=" N VAL A 274 " pdb=" CA VAL A 274 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.21e-02 6.83e+03 9.53e+00 bond pdb=" N LYS A 223 " pdb=" CA LYS A 223 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.31e-02 5.83e+03 9.29e+00 bond pdb=" N VAL A 224 " pdb=" CA VAL A 224 " ideal model delta sigma weight residual 1.460 1.497 -0.036 1.26e-02 6.30e+03 8.36e+00 bond pdb=" N ASN A 148 " pdb=" CA ASN A 148 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.37e+00 ... (remaining 3131 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 3886 1.12 - 2.24: 289 2.24 - 3.36: 55 3.36 - 4.48: 32 4.48 - 5.59: 7 Bond angle restraints: 4269 Sorted by residual: angle pdb=" CA VAL A 224 " pdb=" C VAL A 224 " pdb=" O VAL A 224 " ideal model delta sigma weight residual 120.57 115.75 4.82 1.07e+00 8.73e-01 2.03e+01 angle pdb=" CA GLN A 150 " pdb=" C GLN A 150 " pdb=" O GLN A 150 " ideal model delta sigma weight residual 120.32 115.83 4.49 1.11e+00 8.12e-01 1.64e+01 angle pdb=" CA VAL A 274 " pdb=" C VAL A 274 " pdb=" O VAL A 274 " ideal model delta sigma weight residual 120.85 116.85 4.00 1.06e+00 8.90e-01 1.43e+01 angle pdb=" CA THR A 275 " pdb=" C THR A 275 " pdb=" O THR A 275 " ideal model delta sigma weight residual 119.97 115.76 4.21 1.15e+00 7.56e-01 1.34e+01 angle pdb=" CA PHE A 273 " pdb=" C PHE A 273 " pdb=" O PHE A 273 " ideal model delta sigma weight residual 120.82 117.24 3.58 1.05e+00 9.07e-01 1.16e+01 ... (remaining 4264 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.92: 1699 15.92 - 31.83: 138 31.83 - 47.75: 26 47.75 - 63.66: 2 63.66 - 79.58: 1 Dihedral angle restraints: 1866 sinusoidal: 685 harmonic: 1181 Sorted by residual: dihedral pdb=" CA ILE A 73 " pdb=" C ILE A 73 " pdb=" N SER A 74 " pdb=" CA SER A 74 " ideal model delta harmonic sigma weight residual -180.00 -154.13 -25.87 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA PRO A 109 " pdb=" C PRO A 109 " pdb=" N GLY A 110 " pdb=" CA GLY A 110 " ideal model delta harmonic sigma weight residual -180.00 -154.97 -25.03 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA GLY A 221 " pdb=" C GLY A 221 " pdb=" N VAL A 222 " pdb=" CA VAL A 222 " ideal model delta harmonic sigma weight residual -180.00 -159.02 -20.98 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 1863 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 411 0.053 - 0.106: 109 0.106 - 0.159: 13 0.159 - 0.212: 3 0.212 - 0.266: 2 Chirality restraints: 538 Sorted by residual: chirality pdb=" CB VAL A 224 " pdb=" CA VAL A 224 " pdb=" CG1 VAL A 224 " pdb=" CG2 VAL A 224 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB VAL A 225 " pdb=" CA VAL A 225 " pdb=" CG1 VAL A 225 " pdb=" CG2 VAL A 225 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA GLN A 150 " pdb=" N GLN A 150 " pdb=" C GLN A 150 " pdb=" CB GLN A 150 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.45e-01 ... (remaining 535 not shown) Planarity restraints: 524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 147 " 0.015 2.00e-02 2.50e+03 2.87e-02 8.23e+00 pdb=" C ALA A 147 " -0.050 2.00e-02 2.50e+03 pdb=" O ALA A 147 " 0.019 2.00e-02 2.50e+03 pdb=" N ASN A 148 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 299 " 0.022 2.00e-02 2.50e+03 1.80e-02 6.46e+00 pdb=" CG TYR A 299 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR A 299 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 299 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 299 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 299 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 299 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 299 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 224 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.25e+00 pdb=" C VAL A 224 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL A 224 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL A 225 " 0.013 2.00e-02 2.50e+03 ... (remaining 521 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 560 2.76 - 3.29: 3550 3.29 - 3.83: 4990 3.83 - 4.36: 5548 4.36 - 4.90: 9361 Nonbonded interactions: 24009 Sorted by model distance: nonbonded pdb=" O ALA A 71 " pdb=" OG1 THR A 166 " model vdw 2.223 3.040 nonbonded pdb=" O SER A 278 " pdb=" OG1 THR A 281 " model vdw 2.294 3.040 nonbonded pdb=" O VAL A 151 " pdb=" OG1 THR A 154 " model vdw 2.309 3.040 nonbonded pdb=" O LEU A 228 " pdb=" OG1 THR A 232 " model vdw 2.383 3.040 nonbonded pdb=" O VAL A 412 " pdb=" OG1 THR A 415 " model vdw 2.387 3.040 ... (remaining 24004 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.700 Find NCS groups from input model: 0.030 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 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 : 0.007 0.057 3136 Z= 0.471 Angle : 0.769 5.594 4269 Z= 0.463 Chirality : 0.048 0.266 538 Planarity : 0.005 0.029 524 Dihedral : 11.978 79.581 1116 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % 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 (0.34), residues: 412 helix: -1.19 (0.24), residues: 321 sheet: None (None), residues: 0 loop : -2.03 (0.57), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 114 PHE 0.015 0.002 PHE A 261 TYR 0.043 0.003 TYR A 299 ARG 0.008 0.001 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 84 LYS cc_start: 0.8148 (mmtt) cc_final: 0.7880 (mmmt) REVERT: A 105 ARG cc_start: 0.7068 (mpt-90) cc_final: 0.6704 (ttt-90) REVERT: A 108 ASN cc_start: 0.6656 (m110) cc_final: 0.5520 (t0) REVERT: A 126 GLN cc_start: 0.7441 (tp40) cc_final: 0.6918 (mm110) REVERT: A 273 PHE cc_start: 0.5679 (t80) cc_final: 0.5403 (t80) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1522 time to fit residues: 20.6805 Evaluate side-chains 82 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 0.0000 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS A 108 ASN A 318 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3136 Z= 0.224 Angle : 0.665 5.908 4269 Z= 0.339 Chirality : 0.043 0.157 538 Planarity : 0.004 0.026 524 Dihedral : 5.427 26.228 441 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.84 % Allowed : 13.80 % Favored : 84.36 % 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: 0.72 (0.39), residues: 412 helix: 1.09 (0.27), residues: 328 sheet: None (None), residues: 0 loop : -1.83 (0.57), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 114 PHE 0.015 0.002 PHE A 210 TYR 0.034 0.002 TYR A 299 ARG 0.003 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 108 ASN cc_start: 0.6782 (m-40) cc_final: 0.5632 (t0) REVERT: A 126 GLN cc_start: 0.7309 (tp40) cc_final: 0.6775 (mm110) outliers start: 6 outliers final: 4 residues processed: 88 average time/residue: 0.1172 time to fit residues: 13.1034 Evaluate side-chains 81 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 407 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.4980 chunk 11 optimal weight: 0.0170 chunk 30 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.6418 ------------------------------------------------------------------------------- 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: 0.7641 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3136 Z= 0.222 Angle : 0.647 8.034 4269 Z= 0.324 Chirality : 0.043 0.150 538 Planarity : 0.003 0.022 524 Dihedral : 5.211 25.761 441 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.45 % Allowed : 16.87 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.40), residues: 412 helix: 1.57 (0.28), residues: 330 sheet: None (None), residues: 0 loop : -1.71 (0.59), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 332 PHE 0.015 0.001 PHE A 210 TYR 0.030 0.002 TYR A 299 ARG 0.004 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 0.351 Fit side-chains REVERT: A 108 ASN cc_start: 0.6831 (m-40) cc_final: 0.5598 (t0) REVERT: A 114 HIS cc_start: 0.8270 (OUTLIER) cc_final: 0.8028 (p-80) REVERT: A 126 GLN cc_start: 0.7383 (tp40) cc_final: 0.6836 (mm110) REVERT: A 202 MET cc_start: 0.8600 (mmm) cc_final: 0.8136 (tpp) REVERT: A 273 PHE cc_start: 0.5905 (t80) cc_final: 0.5290 (t80) REVERT: A 351 CYS cc_start: 0.7548 (p) cc_final: 0.6381 (p) outliers start: 8 outliers final: 5 residues processed: 89 average time/residue: 0.1215 time to fit residues: 13.6420 Evaluate side-chains 82 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 76 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 400 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 0.0970 chunk 37 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3136 Z= 0.222 Angle : 0.663 10.396 4269 Z= 0.326 Chirality : 0.043 0.159 538 Planarity : 0.003 0.023 524 Dihedral : 5.167 28.299 441 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.99 % Allowed : 17.18 % Favored : 78.83 % 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: 1.60 (0.41), residues: 412 helix: 1.67 (0.28), residues: 334 sheet: None (None), residues: 0 loop : -1.58 (0.62), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.015 0.002 PHE A 210 TYR 0.028 0.002 TYR A 299 ARG 0.003 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 0.340 Fit side-chains REVERT: A 21 ILE cc_start: 0.8935 (pt) cc_final: 0.8709 (pt) REVERT: A 105 ARG cc_start: 0.6307 (ttt90) cc_final: 0.6034 (ttt-90) REVERT: A 126 GLN cc_start: 0.7513 (tp40) cc_final: 0.6971 (mm110) REVERT: A 202 MET cc_start: 0.8607 (mmm) cc_final: 0.8295 (tpp) REVERT: A 210 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.7707 (t80) outliers start: 13 outliers final: 6 residues processed: 90 average time/residue: 0.1281 time to fit residues: 14.2561 Evaluate side-chains 88 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 400 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 0.0970 chunk 20 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3136 Z= 0.198 Angle : 0.644 10.342 4269 Z= 0.318 Chirality : 0.043 0.151 538 Planarity : 0.003 0.034 524 Dihedral : 5.191 28.080 441 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.37 % Allowed : 19.94 % Favored : 76.69 % 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: 1.68 (0.41), residues: 412 helix: 1.72 (0.28), residues: 333 sheet: None (None), residues: 0 loop : -1.50 (0.64), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.014 0.002 PHE A 210 TYR 0.026 0.002 TYR A 299 ARG 0.002 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 0.346 Fit side-chains REVERT: A 21 ILE cc_start: 0.8971 (pt) cc_final: 0.8702 (pt) REVERT: A 103 MET cc_start: 0.8241 (ttm) cc_final: 0.7979 (ttm) REVERT: A 105 ARG cc_start: 0.6482 (ttt90) cc_final: 0.6141 (ttt-90) REVERT: A 126 GLN cc_start: 0.7505 (tp40) cc_final: 0.6941 (mm110) REVERT: A 155 ILE cc_start: 0.8355 (mt) cc_final: 0.7961 (mt) REVERT: A 202 MET cc_start: 0.8615 (mmm) cc_final: 0.8410 (tpp) REVERT: A 210 PHE cc_start: 0.8465 (OUTLIER) cc_final: 0.7714 (t80) outliers start: 11 outliers final: 8 residues processed: 90 average time/residue: 0.1123 time to fit residues: 12.7611 Evaluate side-chains 92 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 83 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 400 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 0.0980 chunk 20 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3136 Z= 0.220 Angle : 0.667 11.777 4269 Z= 0.328 Chirality : 0.042 0.150 538 Planarity : 0.003 0.024 524 Dihedral : 5.153 27.975 441 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.29 % Allowed : 20.86 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.41), residues: 412 helix: 1.79 (0.28), residues: 332 sheet: None (None), residues: 0 loop : -1.42 (0.64), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.015 0.001 PHE A 210 TYR 0.024 0.002 TYR A 299 ARG 0.003 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 81 time to evaluate : 0.330 Fit side-chains REVERT: A 21 ILE cc_start: 0.9035 (pt) cc_final: 0.8793 (pt) REVERT: A 105 ARG cc_start: 0.6449 (ttt90) cc_final: 0.6062 (ttt-90) REVERT: A 114 HIS cc_start: 0.8128 (p90) cc_final: 0.7790 (p90) REVERT: A 126 GLN cc_start: 0.7484 (tp40) cc_final: 0.6932 (mm110) REVERT: A 210 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.7665 (t80) REVERT: A 269 MET cc_start: 0.7347 (tpp) cc_final: 0.7032 (mmm) outliers start: 14 outliers final: 9 residues processed: 87 average time/residue: 0.1272 time to fit residues: 13.6994 Evaluate side-chains 89 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 400 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 11 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3136 Z= 0.218 Angle : 0.690 12.561 4269 Z= 0.333 Chirality : 0.042 0.150 538 Planarity : 0.004 0.043 524 Dihedral : 5.152 27.491 441 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 4.29 % Allowed : 22.39 % Favored : 73.31 % 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: 1.80 (0.41), residues: 412 helix: 1.80 (0.28), residues: 332 sheet: None (None), residues: 0 loop : -1.40 (0.64), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.015 0.002 PHE A 210 TYR 0.025 0.002 TYR A 299 ARG 0.003 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 0.334 Fit side-chains REVERT: A 21 ILE cc_start: 0.9028 (pt) cc_final: 0.8777 (pt) REVERT: A 52 ARG cc_start: 0.8408 (tpp80) cc_final: 0.6196 (ttp-170) REVERT: A 103 MET cc_start: 0.8059 (ttm) cc_final: 0.7793 (ttm) REVERT: A 105 ARG cc_start: 0.6441 (ttt90) cc_final: 0.6197 (ttt-90) REVERT: A 114 HIS cc_start: 0.8153 (p90) cc_final: 0.7832 (p90) REVERT: A 210 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.7685 (t80) REVERT: A 269 MET cc_start: 0.7301 (tpp) cc_final: 0.6988 (mmm) outliers start: 14 outliers final: 10 residues processed: 92 average time/residue: 0.1181 time to fit residues: 13.6469 Evaluate side-chains 91 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 386 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3136 Z= 0.230 Angle : 0.711 12.902 4269 Z= 0.346 Chirality : 0.043 0.223 538 Planarity : 0.003 0.024 524 Dihedral : 5.127 27.502 441 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.68 % Allowed : 23.93 % Favored : 72.39 % 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: 1.60 (0.41), residues: 412 helix: 1.68 (0.28), residues: 332 sheet: None (None), residues: 0 loop : -1.61 (0.63), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.014 0.001 PHE A 210 TYR 0.027 0.002 TYR A 299 ARG 0.001 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 time to evaluate : 0.338 Fit side-chains REVERT: A 21 ILE cc_start: 0.8845 (pt) cc_final: 0.8557 (pt) REVERT: A 52 ARG cc_start: 0.8389 (tpp80) cc_final: 0.6183 (ttp-170) REVERT: A 103 MET cc_start: 0.8024 (ttm) cc_final: 0.7758 (ttm) REVERT: A 105 ARG cc_start: 0.6441 (ttt90) cc_final: 0.6235 (ttt-90) REVERT: A 114 HIS cc_start: 0.8152 (p90) cc_final: 0.7852 (p90) REVERT: A 269 MET cc_start: 0.7449 (tpp) cc_final: 0.7161 (mmm) outliers start: 12 outliers final: 9 residues processed: 89 average time/residue: 0.1179 time to fit residues: 13.2387 Evaluate side-chains 87 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 386 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 34 optimal weight: 0.0870 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 37 optimal weight: 0.0870 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3136 Z= 0.195 Angle : 0.716 13.846 4269 Z= 0.345 Chirality : 0.044 0.228 538 Planarity : 0.004 0.049 524 Dihedral : 5.088 29.697 441 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.76 % Allowed : 23.93 % Favored : 73.31 % 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: 2.04 (0.42), residues: 412 helix: 2.02 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -1.36 (0.67), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 332 PHE 0.013 0.001 PHE A 210 TYR 0.031 0.002 TYR A 317 ARG 0.001 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.337 Fit side-chains REVERT: A 21 ILE cc_start: 0.8949 (pt) cc_final: 0.8646 (pt) REVERT: A 52 ARG cc_start: 0.8336 (tpp80) cc_final: 0.6124 (ttp-170) REVERT: A 103 MET cc_start: 0.8041 (ttm) cc_final: 0.7804 (ttm) REVERT: A 210 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.7550 (t80) REVERT: A 269 MET cc_start: 0.7401 (tpp) cc_final: 0.7140 (mmm) REVERT: A 276 ARG cc_start: 0.6741 (mtp85) cc_final: 0.6362 (ttp-170) outliers start: 9 outliers final: 7 residues processed: 90 average time/residue: 0.1458 time to fit residues: 16.1299 Evaluate side-chains 89 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 386 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3136 Z= 0.253 Angle : 0.770 13.496 4269 Z= 0.370 Chirality : 0.047 0.224 538 Planarity : 0.004 0.042 524 Dihedral : 5.256 28.038 441 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.45 % Allowed : 25.15 % Favored : 72.39 % 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: 1.82 (0.42), residues: 412 helix: 1.89 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -1.48 (0.67), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.015 0.002 PHE A 210 TYR 0.051 0.002 TYR A 317 ARG 0.006 0.000 ARG A 397 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 0.310 Fit side-chains REVERT: A 52 ARG cc_start: 0.8347 (tpp80) cc_final: 0.6159 (ttp-170) REVERT: A 103 MET cc_start: 0.8087 (ttm) cc_final: 0.7782 (ttm) REVERT: A 210 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.7680 (t80) REVERT: A 269 MET cc_start: 0.7373 (tpp) cc_final: 0.6986 (tpp) REVERT: A 276 ARG cc_start: 0.6742 (mtp85) cc_final: 0.6371 (ttp-170) outliers start: 8 outliers final: 6 residues processed: 85 average time/residue: 0.1280 time to fit residues: 13.4244 Evaluate side-chains 87 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 386 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.164626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.135384 restraints weight = 5545.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.137838 restraints weight = 3676.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.139453 restraints weight = 2810.327| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.5106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3136 Z= 0.248 Angle : 0.770 13.592 4269 Z= 0.372 Chirality : 0.048 0.294 538 Planarity : 0.004 0.037 524 Dihedral : 5.346 29.534 441 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.76 % Allowed : 26.07 % Favored : 71.17 % 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: 1.75 (0.42), residues: 412 helix: 1.83 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -1.48 (0.67), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.015 0.002 PHE A 210 TYR 0.063 0.002 TYR A 317 ARG 0.004 0.000 ARG A 397 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1036.54 seconds wall clock time: 19 minutes 8.98 seconds (1148.98 seconds total)