Starting phenix.real_space_refine on Sun Mar 10 15:37:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyk_21967/03_2024/6wyk_21967.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyk_21967/03_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_21967/03_2024/6wyk_21967.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyk_21967/03_2024/6wyk_21967.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyk_21967/03_2024/6wyk_21967.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyk_21967/03_2024/6wyk_21967.pdb" } 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 Residue "A TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A ASP 185": "OD1" <-> "OD2" Residue "A ASP 257": "OD1" <-> "OD2" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "A PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 376": "OD1" <-> "OD2" Residue "A TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 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: 2.15, per 1000 atoms: 0.70 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 - 3.50 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: 1.31 Conformation dependent library (CDL) restraints added in 654.2 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: 0.37 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: 0.86 Time building geometry restraints manager: 1.42 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: 98.27 - 104.90: 65 104.90 - 111.52: 1514 111.52 - 118.15: 932 118.15 - 124.77: 1733 124.77 - 131.40: 25 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 2.440 nonbonded pdb=" O SER A 278 " pdb=" OG1 THR A 281 " model vdw 2.294 2.440 nonbonded pdb=" O VAL A 151 " pdb=" OG1 THR A 154 " model vdw 2.309 2.440 nonbonded pdb=" O LEU A 228 " pdb=" OG1 THR A 232 " model vdw 2.383 2.440 nonbonded pdb=" O VAL A 412 " pdb=" OG1 THR A 415 " model vdw 2.387 2.440 ... (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: 0.740 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: 3.430 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.710 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.970 ------------------------------------------------------------------------------- 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 : 0.344 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: 0.1476 time to fit residues: 20.1388 Evaluate side-chains 82 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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: 0.4980 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3136 Z= 0.223 Angle : 0.662 6.204 4269 Z= 0.337 Chirality : 0.042 0.150 538 Planarity : 0.004 0.025 524 Dihedral : 5.421 25.515 441 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.45 % Allowed : 12.58 % Favored : 84.97 % 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: 0.65 (0.39), residues: 412 helix: 1.04 (0.27), residues: 328 sheet: None (None), residues: 0 loop : -1.87 (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 0.002 0.000 ARG A 276 *********************** 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 95 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 105 ARG cc_start: 0.7044 (mpt-90) cc_final: 0.6840 (ttt-90) REVERT: A 126 GLN cc_start: 0.7352 (tp40) cc_final: 0.6790 (mm110) outliers start: 8 outliers final: 7 residues processed: 89 average time/residue: 0.1177 time to fit residues: 13.2461 Evaluate side-chains 84 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 355 VAL 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: 0.8980 chunk 11 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 25 optimal weight: 0.0470 chunk 10 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 12 optimal weight: 0.0980 chunk 29 optimal weight: 0.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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: 0.7610 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3136 Z= 0.204 Angle : 0.640 7.984 4269 Z= 0.318 Chirality : 0.042 0.173 538 Planarity : 0.003 0.022 524 Dihedral : 5.178 29.274 441 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.07 % Allowed : 17.79 % Favored : 79.14 % 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: 1.53 (0.40), residues: 412 helix: 1.68 (0.28), residues: 330 sheet: None (None), residues: 0 loop : -1.75 (0.58), residues: 82 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 0.030 0.002 TYR A 299 ARG 0.002 0.000 ARG A 276 *********************** 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 95 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 0.347 Fit side-chains REVERT: A 126 GLN cc_start: 0.7454 (tp40) cc_final: 0.6870 (mm110) REVERT: A 202 MET cc_start: 0.8470 (mmm) cc_final: 0.8159 (tpp) REVERT: A 219 GLU cc_start: 0.7733 (tp30) cc_final: 0.7471 (mm-30) REVERT: A 351 CYS cc_start: 0.7579 (p) cc_final: 0.6840 (p) outliers start: 10 outliers final: 7 residues processed: 87 average time/residue: 0.1131 time to fit residues: 12.6559 Evaluate side-chains 87 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 308 THR Chi-restraints excluded: chain A residue 312 ASP 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: 1.9990 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 39 optimal weight: 0.5980 chunk 35 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.7637 moved from start: 0.3457 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= 0.219 Angle : 0.641 9.695 4269 Z= 0.316 Chirality : 0.042 0.153 538 Planarity : 0.003 0.024 524 Dihedral : 5.110 29.164 441 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % 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: 1.85 (0.41), residues: 412 helix: 1.89 (0.29), residues: 330 sheet: None (None), residues: 0 loop : -1.56 (0.60), residues: 82 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 0.028 0.002 TYR A 299 ARG 0.001 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 94 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 0.427 Fit side-chains REVERT: A 126 GLN cc_start: 0.7597 (tp40) cc_final: 0.7000 (mm110) REVERT: A 202 MET cc_start: 0.8516 (mmm) cc_final: 0.8291 (tpp) REVERT: A 210 PHE cc_start: 0.8482 (OUTLIER) cc_final: 0.7746 (t80) REVERT: A 269 MET cc_start: 0.7408 (tpp) cc_final: 0.7073 (mmm) outliers start: 13 outliers final: 8 residues processed: 88 average time/residue: 0.1125 time to fit residues: 12.8351 Evaluate side-chains 87 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 78 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 312 ASP 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: 2.9990 chunk 0 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 0.0970 chunk 20 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.0050 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3136 Z= 0.196 Angle : 0.635 12.028 4269 Z= 0.310 Chirality : 0.042 0.157 538 Planarity : 0.004 0.046 524 Dihedral : 5.009 28.552 441 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.07 % Allowed : 20.25 % 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: 2.06 (0.42), residues: 412 helix: 1.99 (0.28), residues: 332 sheet: None (None), residues: 0 loop : -1.34 (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 0.026 0.001 TYR A 299 ARG 0.001 0.000 ARG A 52 *********************** 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: 10 poor density : 87 time to evaluate : 0.368 Fit side-chains REVERT: A 103 MET cc_start: 0.8104 (ttm) cc_final: 0.7882 (ttm) REVERT: A 126 GLN cc_start: 0.7600 (tp40) cc_final: 0.6993 (mm110) REVERT: A 210 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.7674 (t80) REVERT: A 362 MET cc_start: 0.7832 (mtm) cc_final: 0.7528 (mtp) outliers start: 10 outliers final: 9 residues processed: 89 average time/residue: 0.1251 time to fit residues: 13.9474 Evaluate side-chains 92 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 198 VAL Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 312 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.4980 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 0.2980 chunk 20 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.4086 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= 0.204 Angle : 0.659 11.277 4269 Z= 0.318 Chirality : 0.042 0.165 538 Planarity : 0.003 0.024 524 Dihedral : 4.935 29.019 441 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.37 % Allowed : 21.47 % Favored : 75.15 % 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: 2.03 (0.42), residues: 412 helix: 1.95 (0.28), residues: 332 sheet: None (None), residues: 0 loop : -1.24 (0.65), 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 0.026 0.002 TYR A 299 ARG 0.002 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: 11 poor density : 84 time to evaluate : 0.310 Fit side-chains REVERT: A 21 ILE cc_start: 0.8875 (pt) cc_final: 0.8561 (pt) REVERT: A 126 GLN cc_start: 0.7606 (tp40) cc_final: 0.6974 (mm110) REVERT: A 210 PHE cc_start: 0.8481 (OUTLIER) cc_final: 0.7663 (t80) REVERT: A 269 MET cc_start: 0.8028 (tpp) cc_final: 0.7681 (mmm) outliers start: 11 outliers final: 9 residues processed: 88 average time/residue: 0.1177 time to fit residues: 13.0208 Evaluate side-chains 91 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 210 PHE Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 312 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 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 318 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3136 Z= 0.234 Angle : 0.684 11.613 4269 Z= 0.331 Chirality : 0.043 0.163 538 Planarity : 0.004 0.054 524 Dihedral : 5.053 28.426 441 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 5.52 % Allowed : 22.70 % Favored : 71.78 % 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: 1.90 (0.42), residues: 412 helix: 1.88 (0.28), residues: 331 sheet: None (None), residues: 0 loop : -1.37 (0.65), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 32 PHE 0.016 0.002 PHE A 210 TYR 0.025 0.002 TYR A 299 ARG 0.001 0.000 ARG A 52 *********************** 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 105 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 87 time to evaluate : 0.341 Fit side-chains REVERT: A 21 ILE cc_start: 0.8900 (pt) cc_final: 0.8608 (pt) REVERT: A 52 ARG cc_start: 0.8480 (tpp80) cc_final: 0.6235 (ttp-170) REVERT: A 103 MET cc_start: 0.8065 (ttm) cc_final: 0.7792 (ttm) REVERT: A 210 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.7704 (t80) outliers start: 18 outliers final: 13 residues processed: 95 average time/residue: 0.1185 time to fit residues: 14.2049 Evaluate side-chains 95 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 81 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 308 THR Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 339 LEU 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 Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 400 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3136 Z= 0.242 Angle : 0.732 12.330 4269 Z= 0.348 Chirality : 0.043 0.159 538 Planarity : 0.003 0.025 524 Dihedral : 5.140 29.079 441 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.60 % Allowed : 24.54 % Favored : 70.86 % 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: 1.92 (0.42), residues: 412 helix: 1.89 (0.28), residues: 325 sheet: None (None), residues: 0 loop : -1.11 (0.67), residues: 87 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 0.001 0.000 ARG A 77 *********************** 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 97 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 0.319 Fit side-chains REVERT: A 21 ILE cc_start: 0.8894 (pt) cc_final: 0.8604 (pt) REVERT: A 52 ARG cc_start: 0.8418 (tpp80) cc_final: 0.6219 (ttp-170) REVERT: A 103 MET cc_start: 0.8065 (ttm) cc_final: 0.7790 (ttm) REVERT: A 185 ASP cc_start: 0.7808 (m-30) cc_final: 0.6795 (t0) REVERT: A 210 PHE cc_start: 0.8499 (OUTLIER) cc_final: 0.7688 (t80) REVERT: A 269 MET cc_start: 0.7745 (tpp) cc_final: 0.7533 (mmm) outliers start: 15 outliers final: 12 residues processed: 88 average time/residue: 0.1213 time to fit residues: 13.5399 Evaluate side-chains 95 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 308 THR Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 339 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.1980 chunk 33 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 0.0980 chunk 40 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3136 Z= 0.211 Angle : 0.709 12.178 4269 Z= 0.338 Chirality : 0.042 0.160 538 Planarity : 0.004 0.049 524 Dihedral : 5.071 28.895 441 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.29 % Allowed : 24.85 % Favored : 70.86 % 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: 1.97 (0.42), residues: 412 helix: 1.93 (0.28), residues: 326 sheet: None (None), residues: 0 loop : -1.13 (0.67), residues: 86 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 0.025 0.002 TYR A 299 ARG 0.001 0.000 ARG A 105 *********************** 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 95 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 81 time to evaluate : 0.345 Fit side-chains REVERT: A 21 ILE cc_start: 0.8961 (pt) cc_final: 0.8681 (pt) REVERT: A 52 ARG cc_start: 0.8382 (tpp80) cc_final: 0.6208 (ttp-170) REVERT: A 103 MET cc_start: 0.8070 (ttm) cc_final: 0.7813 (ttm) REVERT: A 210 PHE cc_start: 0.8449 (OUTLIER) cc_final: 0.7665 (t80) REVERT: A 276 ARG cc_start: 0.6534 (mtp85) cc_final: 0.6230 (ttp-170) outliers start: 14 outliers final: 12 residues processed: 88 average time/residue: 0.1350 time to fit residues: 14.7037 Evaluate side-chains 94 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 210 PHE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 312 ASP 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 Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 400 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 13 optimal weight: 0.1980 chunk 33 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.4824 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= 0.217 Angle : 0.715 12.547 4269 Z= 0.339 Chirality : 0.042 0.162 538 Planarity : 0.004 0.045 524 Dihedral : 5.049 28.907 441 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.99 % Allowed : 24.85 % 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: 2.03 (0.42), residues: 412 helix: 1.99 (0.28), residues: 325 sheet: None (None), residues: 0 loop : -1.19 (0.67), residues: 87 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 0.027 0.002 TYR A 299 ARG 0.001 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 99 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 0.331 Fit side-chains REVERT: A 21 ILE cc_start: 0.8975 (pt) cc_final: 0.8680 (pt) REVERT: A 52 ARG cc_start: 0.8335 (tpp80) cc_final: 0.6129 (ttp-170) REVERT: A 103 MET cc_start: 0.8045 (ttm) cc_final: 0.7787 (ttm) REVERT: A 210 PHE cc_start: 0.8450 (OUTLIER) cc_final: 0.7636 (t80) REVERT: A 276 ARG cc_start: 0.6484 (mtp85) cc_final: 0.6203 (ttp-170) outliers start: 13 outliers final: 12 residues processed: 93 average time/residue: 0.1395 time to fit residues: 16.0610 Evaluate side-chains 96 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 210 PHE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 312 ASP 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 Chi-restraints excluded: chain A residue 400 VAL 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: 0.8980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3952 r_free = 0.3952 target = 0.164882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.135603 restraints weight = 5521.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.137924 restraints weight = 3740.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.139680 restraints weight = 2897.970| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4949 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= 0.217 Angle : 0.717 12.636 4269 Z= 0.339 Chirality : 0.042 0.165 538 Planarity : 0.004 0.040 524 Dihedral : 5.046 28.734 441 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.29 % Allowed : 24.85 % Favored : 70.86 % 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: 2.01 (0.42), residues: 412 helix: 1.98 (0.28), residues: 325 sheet: None (None), residues: 0 loop : -1.20 (0.67), residues: 87 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 0.026 0.002 TYR A 299 ARG 0.001 0.000 ARG A 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1020.67 seconds wall clock time: 19 minutes 9.54 seconds (1149.54 seconds total)