Starting phenix.real_space_refine on Thu Jul 18 18:37:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xo9_38523/07_2024/8xo9_38523.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xo9_38523/07_2024/8xo9_38523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xo9_38523/07_2024/8xo9_38523.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xo9_38523/07_2024/8xo9_38523.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xo9_38523/07_2024/8xo9_38523.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xo9_38523/07_2024/8xo9_38523.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.057 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 27 5.16 5 C 1937 2.51 5 N 454 2.21 5 O 490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 127": "OE1" <-> "OE2" Residue "A PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 262": "OD1" <-> "OD2" Residue "A GLU 312": "OE1" <-> "OE2" Residue "A PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 2908 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 2896 Classifications: {'peptide': 392} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 23, 'TRANS': 368} Chain breaks: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'E5E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.96, per 1000 atoms: 1.02 Number of scatterers: 2908 At special positions: 0 Unit cell: (54.4, 71.4, 75.65, 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 27 16.00 O 490 8.00 N 454 7.00 C 1937 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: 1.02 Conformation dependent library (CDL) restraints added in 708.0 milliseconds 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 708 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 91.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 19 through 54 removed outlier: 4.147A pdb=" N VAL A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Proline residue: A 42 - end of helix Proline residue: A 45 - end of helix Processing helix chain 'A' and resid 124 through 157 removed outlier: 3.881A pdb=" N LEU A 133 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 3.894A pdb=" N GLY A 150 " --> pdb=" O ASN A 146 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 151 " --> pdb=" O PRO A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 178 removed outlier: 3.640A pdb=" N PHE A 166 " --> pdb=" O ILE A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 211 removed outlier: 3.657A pdb=" N LEU A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 246 removed outlier: 3.737A pdb=" N ASN A 219 " --> pdb=" O GLU A 215 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY A 222 " --> pdb=" O GLY A 218 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 234 " --> pdb=" O MET A 230 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY A 235 " --> pdb=" O GLY A 231 " (cutoff:3.500A) Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 249 through 269 Processing helix chain 'A' and resid 284 through 290 Processing helix chain 'A' and resid 291 through 312 removed outlier: 4.157A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 323 Processing helix chain 'A' and resid 328 through 333 removed outlier: 4.149A pdb=" N VAL A 332 " --> pdb=" O TRP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 356 removed outlier: 4.052A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N HIS A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LYS A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 375 Processing helix chain 'A' and resid 376 through 378 No H-bonds generated for 'chain 'A' and resid 376 through 378' Processing helix chain 'A' and resid 380 through 383 Processing helix chain 'A' and resid 384 through 414 removed outlier: 3.604A pdb=" N ASN A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 417 through 447 removed outlier: 4.342A pdb=" N VAL A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TYR A 422 " --> pdb=" O TYR A 418 " (cutoff:3.500A) Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 448 through 464 removed outlier: 3.610A pdb=" N LEU A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 470 removed outlier: 3.734A pdb=" N PHE A 469 " --> pdb=" O LEU A 466 " (cutoff:3.500A) 244 hydrogen bonds defined for protein. 723 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: 0.79 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 870 1.34 - 1.46: 645 1.46 - 1.58: 1416 1.58 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 2977 Sorted by residual: bond pdb=" CAJ E5E A 601 " pdb=" OAC E5E A 601 " ideal model delta sigma weight residual 1.350 1.401 -0.051 2.00e-02 2.50e+03 6.57e+00 bond pdb=" N MET A 175 " pdb=" CA MET A 175 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.19e+00 bond pdb=" N MET A 431 " pdb=" CA MET A 431 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.83e+00 bond pdb=" N PHE A 176 " pdb=" CA PHE A 176 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.76e+00 bond pdb=" CAI E5E A 601 " pdb=" OAB E5E A 601 " ideal model delta sigma weight residual 1.354 1.401 -0.047 2.00e-02 2.50e+03 5.45e+00 ... (remaining 2972 not shown) Histogram of bond angle deviations from ideal: 99.86 - 106.69: 115 106.69 - 113.52: 1640 113.52 - 120.35: 1166 120.35 - 127.18: 1100 127.18 - 134.01: 32 Bond angle restraints: 4053 Sorted by residual: angle pdb=" C ALA A 177 " pdb=" N PHE A 178 " pdb=" CA PHE A 178 " ideal model delta sigma weight residual 122.86 116.34 6.52 1.53e+00 4.27e-01 1.81e+01 angle pdb=" CA MET A 175 " pdb=" C MET A 175 " pdb=" O MET A 175 " ideal model delta sigma weight residual 120.82 117.57 3.25 1.05e+00 9.07e-01 9.60e+00 angle pdb=" C ASP A 123 " pdb=" N LEU A 124 " pdb=" CA LEU A 124 " ideal model delta sigma weight residual 121.54 127.10 -5.56 1.91e+00 2.74e-01 8.47e+00 angle pdb=" CA ILE A 447 " pdb=" C ILE A 447 " pdb=" N GLY A 448 " ideal model delta sigma weight residual 116.60 120.72 -4.12 1.45e+00 4.76e-01 8.09e+00 angle pdb=" CA PHE A 176 " pdb=" CB PHE A 176 " pdb=" CG PHE A 176 " ideal model delta sigma weight residual 113.80 116.62 -2.82 1.00e+00 1.00e+00 7.97e+00 ... (remaining 4048 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 1539 17.52 - 35.04: 165 35.04 - 52.57: 37 52.57 - 70.09: 2 70.09 - 87.61: 1 Dihedral angle restraints: 1744 sinusoidal: 634 harmonic: 1110 Sorted by residual: dihedral pdb=" CA LEU A 270 " pdb=" C LEU A 270 " pdb=" N GLN A 271 " pdb=" CA GLN A 271 " ideal model delta harmonic sigma weight residual 180.00 160.96 19.04 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CB GLU A 127 " pdb=" CG GLU A 127 " pdb=" CD GLU A 127 " pdb=" OE1 GLU A 127 " ideal model delta sinusoidal sigma weight residual 0.00 -87.61 87.61 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CA PRO A 42 " pdb=" C PRO A 42 " pdb=" N ILE A 43 " pdb=" CA ILE A 43 " ideal model delta harmonic sigma weight residual -180.00 -164.09 -15.91 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 1741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 360 0.044 - 0.088: 104 0.088 - 0.132: 22 0.132 - 0.177: 1 0.177 - 0.221: 2 Chirality restraints: 489 Sorted by residual: chirality pdb=" CA PHE A 176 " pdb=" N PHE A 176 " pdb=" C PHE A 176 " pdb=" CB PHE A 176 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CAL E5E A 601 " pdb=" CAH E5E A 601 " pdb=" CAK E5E A 601 " pdb=" OAD E5E A 601 " both_signs ideal model delta sigma weight residual False -2.31 -2.51 0.20 2.00e-01 2.50e+01 9.88e-01 chirality pdb=" CA PHE A 348 " pdb=" N PHE A 348 " pdb=" C PHE A 348 " pdb=" CB PHE A 348 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.38e-01 ... (remaining 486 not shown) Planarity restraints: 496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 124 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.17e+00 pdb=" C LEU A 124 " -0.052 2.00e-02 2.50e+03 pdb=" O LEU A 124 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU A 125 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 235 " 0.042 5.00e-02 4.00e+02 6.25e-02 6.26e+00 pdb=" N PRO A 236 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 236 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 236 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 473 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO A 474 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 474 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 474 " 0.031 5.00e-02 4.00e+02 ... (remaining 493 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 747 2.81 - 3.33: 2964 3.33 - 3.85: 4782 3.85 - 4.38: 4949 4.38 - 4.90: 9157 Nonbonded interactions: 22599 Sorted by model distance: nonbonded pdb=" OG SER A 325 " pdb=" OE1 GLN A 329 " model vdw 2.284 2.440 nonbonded pdb=" OD2 ASP A 33 " pdb=" OG SER A 196 " model vdw 2.519 2.440 nonbonded pdb=" OG SER A 181 " pdb=" N TYR A 182 " model vdw 2.545 2.520 nonbonded pdb=" O ALA A 333 " pdb=" ND2 ASN A 388 " model vdw 2.568 2.520 nonbonded pdb=" O PRO A 473 " pdb=" CA PRO A 474 " model vdw 2.582 2.776 ... (remaining 22594 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.850 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 2977 Z= 0.272 Angle : 0.739 9.662 4053 Z= 0.391 Chirality : 0.043 0.221 489 Planarity : 0.006 0.063 496 Dihedral : 14.590 87.612 1036 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 21.12 % Favored : 78.88 % 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: 1.96 (0.44), residues: 388 helix: 1.80 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -1.67 (0.75), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 318 HIS 0.006 0.002 HIS A 53 PHE 0.019 0.002 PHE A 468 TYR 0.013 0.001 TYR A 49 ARG 0.005 0.001 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.297 Fit side-chains REVERT: A 225 LEU cc_start: 0.7535 (mm) cc_final: 0.6771 (tt) REVERT: A 244 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8344 (tm-30) REVERT: A 405 ILE cc_start: 0.8787 (mm) cc_final: 0.8555 (mt) REVERT: A 431 MET cc_start: 0.8307 (mmt) cc_final: 0.8028 (mmt) REVERT: A 459 ILE cc_start: 0.7168 (mt) cc_final: 0.6903 (mm) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1308 time to fit residues: 7.4657 Evaluate side-chains 44 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 22 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 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 53 HIS A 192 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.0802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2977 Z= 0.224 Angle : 0.667 9.631 4053 Z= 0.326 Chirality : 0.041 0.147 489 Planarity : 0.006 0.054 496 Dihedral : 5.524 34.416 416 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.65 % Allowed : 20.79 % Favored : 77.56 % 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: 2.30 (0.45), residues: 388 helix: 2.17 (0.30), residues: 324 sheet: None (None), residues: 0 loop : -2.04 (0.69), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 328 HIS 0.005 0.001 HIS A 53 PHE 0.016 0.002 PHE A 27 TYR 0.009 0.001 TYR A 49 ARG 0.003 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 0.283 Fit side-chains REVERT: A 225 LEU cc_start: 0.7482 (mm) cc_final: 0.6504 (tt) REVERT: A 405 ILE cc_start: 0.8784 (mm) cc_final: 0.8543 (mt) REVERT: A 431 MET cc_start: 0.8329 (mmt) cc_final: 0.8049 (mmt) REVERT: A 459 ILE cc_start: 0.7216 (mt) cc_final: 0.6938 (mm) outliers start: 5 outliers final: 3 residues processed: 48 average time/residue: 0.1209 time to fit residues: 7.4177 Evaluate side-chains 45 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 283 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.0060 chunk 10 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 0.0000 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 overall best weight: 0.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2977 Z= 0.200 Angle : 0.643 9.620 4053 Z= 0.309 Chirality : 0.040 0.137 489 Planarity : 0.006 0.051 496 Dihedral : 4.627 18.843 416 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.30 % Allowed : 19.14 % Favored : 77.56 % 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: 2.47 (0.45), residues: 388 helix: 2.26 (0.30), residues: 326 sheet: None (None), residues: 0 loop : -1.97 (0.70), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 328 HIS 0.005 0.002 HIS A 53 PHE 0.014 0.002 PHE A 27 TYR 0.009 0.001 TYR A 49 ARG 0.003 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 44 time to evaluate : 0.317 Fit side-chains REVERT: A 225 LEU cc_start: 0.7419 (mm) cc_final: 0.6431 (tt) REVERT: A 253 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6449 (mp) REVERT: A 431 MET cc_start: 0.8272 (mmt) cc_final: 0.8012 (mmt) REVERT: A 459 ILE cc_start: 0.7208 (OUTLIER) cc_final: 0.6920 (mm) outliers start: 10 outliers final: 5 residues processed: 52 average time/residue: 0.1122 time to fit residues: 7.5724 Evaluate side-chains 49 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 459 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 23 optimal weight: 0.3980 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 0.0570 chunk 33 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2977 Z= 0.190 Angle : 0.637 9.599 4053 Z= 0.304 Chirality : 0.040 0.135 489 Planarity : 0.006 0.052 496 Dihedral : 4.366 17.924 416 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.31 % Allowed : 20.79 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.45), residues: 388 helix: 2.35 (0.30), residues: 326 sheet: None (None), residues: 0 loop : -1.97 (0.70), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 328 HIS 0.005 0.001 HIS A 53 PHE 0.014 0.001 PHE A 27 TYR 0.008 0.001 TYR A 49 ARG 0.002 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.308 Fit side-chains REVERT: A 225 LEU cc_start: 0.7415 (mm) cc_final: 0.6450 (tt) REVERT: A 431 MET cc_start: 0.8220 (mmt) cc_final: 0.8010 (tpt) REVERT: A 459 ILE cc_start: 0.7212 (mt) cc_final: 0.6907 (mm) outliers start: 7 outliers final: 4 residues processed: 50 average time/residue: 0.1016 time to fit residues: 6.7442 Evaluate side-chains 46 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 283 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.7980 chunk 15 optimal weight: 0.0870 chunk 32 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 0.0170 chunk 33 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2977 Z= 0.186 Angle : 0.646 9.579 4053 Z= 0.305 Chirality : 0.040 0.132 489 Planarity : 0.006 0.051 496 Dihedral : 4.288 18.247 416 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.30 % Allowed : 19.80 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.45), residues: 388 helix: 2.40 (0.30), residues: 326 sheet: None (None), residues: 0 loop : -1.92 (0.72), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 318 HIS 0.001 0.001 HIS A 53 PHE 0.015 0.001 PHE A 27 TYR 0.011 0.001 TYR A 49 ARG 0.002 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 44 time to evaluate : 0.320 Fit side-chains REVERT: A 225 LEU cc_start: 0.7298 (mm) cc_final: 0.6274 (tt) REVERT: A 253 LEU cc_start: 0.6722 (OUTLIER) cc_final: 0.6500 (mp) REVERT: A 405 ILE cc_start: 0.8753 (mm) cc_final: 0.8496 (mt) REVERT: A 431 MET cc_start: 0.8228 (mmt) cc_final: 0.8014 (tpt) REVERT: A 459 ILE cc_start: 0.7231 (OUTLIER) cc_final: 0.6920 (mm) outliers start: 10 outliers final: 7 residues processed: 52 average time/residue: 0.0873 time to fit residues: 6.0957 Evaluate side-chains 52 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 43 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 459 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 0.1980 chunk 36 optimal weight: 0.3980 chunk 4 optimal weight: 0.0570 chunk 21 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2977 Z= 0.183 Angle : 0.638 9.581 4053 Z= 0.302 Chirality : 0.040 0.131 489 Planarity : 0.006 0.052 496 Dihedral : 4.212 17.679 416 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.29 % Allowed : 20.46 % Favored : 75.25 % 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: 2.75 (0.45), residues: 388 helix: 2.45 (0.30), residues: 326 sheet: None (None), residues: 0 loop : -1.85 (0.73), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 328 HIS 0.002 0.001 HIS A 53 PHE 0.014 0.001 PHE A 27 TYR 0.010 0.001 TYR A 49 ARG 0.001 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 44 time to evaluate : 0.310 Fit side-chains REVERT: A 225 LEU cc_start: 0.7195 (mm) cc_final: 0.6224 (tt) REVERT: A 397 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.7412 (mtm) REVERT: A 403 MET cc_start: 0.8454 (mmt) cc_final: 0.8243 (mmt) REVERT: A 405 ILE cc_start: 0.8729 (mm) cc_final: 0.8463 (mt) REVERT: A 431 MET cc_start: 0.8208 (mmt) cc_final: 0.7995 (tpt) REVERT: A 459 ILE cc_start: 0.7230 (mt) cc_final: 0.6914 (mm) outliers start: 13 outliers final: 5 residues processed: 55 average time/residue: 0.1135 time to fit residues: 8.0883 Evaluate side-chains 50 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 415 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 23 optimal weight: 0.4980 chunk 22 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 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 34 ASN A 53 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2977 Z= 0.228 Angle : 0.676 9.873 4053 Z= 0.322 Chirality : 0.041 0.134 489 Planarity : 0.006 0.057 496 Dihedral : 4.306 18.257 416 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.62 % Allowed : 21.12 % Favored : 74.26 % 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: 2.60 (0.45), residues: 388 helix: 2.38 (0.30), residues: 325 sheet: None (None), residues: 0 loop : -2.00 (0.69), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 318 HIS 0.002 0.001 HIS A 53 PHE 0.014 0.001 PHE A 27 TYR 0.011 0.001 TYR A 49 ARG 0.001 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 45 time to evaluate : 0.279 Fit side-chains REVERT: A 225 LEU cc_start: 0.7273 (mm) cc_final: 0.6258 (tt) REVERT: A 397 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.7400 (mtm) REVERT: A 405 ILE cc_start: 0.8772 (mm) cc_final: 0.8512 (mt) REVERT: A 431 MET cc_start: 0.8224 (mmt) cc_final: 0.8003 (tpt) outliers start: 14 outliers final: 10 residues processed: 56 average time/residue: 0.1090 time to fit residues: 7.8828 Evaluate side-chains 54 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 43 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 459 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 0.0060 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 10 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 53 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2977 Z= 0.196 Angle : 0.659 10.351 4053 Z= 0.313 Chirality : 0.040 0.130 489 Planarity : 0.006 0.057 496 Dihedral : 4.253 17.712 416 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.63 % Allowed : 22.11 % Favored : 74.26 % 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: 2.67 (0.45), residues: 388 helix: 2.42 (0.30), residues: 326 sheet: None (None), residues: 0 loop : -2.04 (0.69), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 328 HIS 0.001 0.001 HIS A 353 PHE 0.015 0.001 PHE A 27 TYR 0.010 0.001 TYR A 49 ARG 0.001 0.000 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 45 time to evaluate : 0.292 Fit side-chains REVERT: A 225 LEU cc_start: 0.7128 (mm) cc_final: 0.6172 (tt) REVERT: A 397 MET cc_start: 0.7621 (OUTLIER) cc_final: 0.7410 (mtm) REVERT: A 405 ILE cc_start: 0.8752 (mm) cc_final: 0.8490 (mt) REVERT: A 431 MET cc_start: 0.8209 (mmt) cc_final: 0.7988 (tpt) REVERT: A 459 ILE cc_start: 0.7220 (OUTLIER) cc_final: 0.6912 (mm) outliers start: 11 outliers final: 8 residues processed: 53 average time/residue: 0.1124 time to fit residues: 7.6820 Evaluate side-chains 55 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 45 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 459 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.0000 chunk 34 optimal weight: 0.6980 chunk 23 optimal weight: 0.4980 chunk 37 optimal weight: 0.2980 chunk 22 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 0.0670 chunk 38 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.2922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2977 Z= 0.169 Angle : 0.659 9.865 4053 Z= 0.310 Chirality : 0.040 0.130 489 Planarity : 0.006 0.050 496 Dihedral : 4.203 17.976 416 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.63 % Allowed : 22.44 % Favored : 73.93 % 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: 2.81 (0.45), residues: 388 helix: 2.52 (0.30), residues: 327 sheet: None (None), residues: 0 loop : -2.06 (0.70), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 328 HIS 0.004 0.001 HIS A 353 PHE 0.014 0.001 PHE A 27 TYR 0.011 0.001 TYR A 49 ARG 0.002 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 50 time to evaluate : 0.325 Fit side-chains REVERT: A 225 LEU cc_start: 0.7060 (mm) cc_final: 0.6142 (tt) REVERT: A 397 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.7369 (mtm) REVERT: A 459 ILE cc_start: 0.7198 (mt) cc_final: 0.6887 (mm) outliers start: 11 outliers final: 8 residues processed: 58 average time/residue: 0.1142 time to fit residues: 8.5324 Evaluate side-chains 55 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 46 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 415 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.3980 chunk 18 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 0.0980 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2977 Z= 0.216 Angle : 0.687 9.871 4053 Z= 0.325 Chirality : 0.041 0.130 489 Planarity : 0.006 0.056 496 Dihedral : 4.237 17.751 416 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.30 % Allowed : 22.77 % Favored : 73.93 % 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: 2.57 (0.45), residues: 388 helix: 2.35 (0.30), residues: 326 sheet: None (None), residues: 0 loop : -2.04 (0.69), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 318 HIS 0.001 0.001 HIS A 53 PHE 0.012 0.001 PHE A 27 TYR 0.011 0.001 TYR A 49 ARG 0.001 0.000 ARG A 155 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 47 time to evaluate : 0.306 Fit side-chains REVERT: A 221 MET cc_start: 0.7402 (mmp) cc_final: 0.6248 (ttt) REVERT: A 225 LEU cc_start: 0.7099 (mm) cc_final: 0.6129 (tt) REVERT: A 397 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.7424 (mtm) REVERT: A 405 ILE cc_start: 0.8741 (mm) cc_final: 0.8479 (mt) outliers start: 10 outliers final: 8 residues processed: 54 average time/residue: 0.1062 time to fit residues: 7.4708 Evaluate side-chains 55 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 46 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 415 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 20 optimal weight: 0.0980 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3871 r_free = 0.3871 target = 0.161246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.133145 restraints weight = 3727.067| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.25 r_work: 0.3469 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2977 Z= 0.202 Angle : 0.682 9.822 4053 Z= 0.323 Chirality : 0.041 0.128 489 Planarity : 0.006 0.055 496 Dihedral : 4.272 17.978 416 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.30 % Allowed : 22.77 % Favored : 73.93 % 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: 2.54 (0.45), residues: 388 helix: 2.32 (0.30), residues: 326 sheet: None (None), residues: 0 loop : -2.02 (0.69), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 328 HIS 0.001 0.001 HIS A 414 PHE 0.013 0.001 PHE A 27 TYR 0.011 0.001 TYR A 49 ARG 0.002 0.000 ARG A 155 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1023.53 seconds wall clock time: 20 minutes 51.75 seconds (1251.75 seconds total)