Starting phenix.real_space_refine on Mon Jun 24 14:20:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xo9_38523/06_2024/8xo9_38523_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xo9_38523/06_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_38523/06_2024/8xo9_38523.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xo9_38523/06_2024/8xo9_38523.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xo9_38523/06_2024/8xo9_38523_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xo9_38523/06_2024/8xo9_38523_updated.pdb" } 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-5370/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: 2.86, per 1000 atoms: 0.98 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: 1.18 Conformation dependent library (CDL) restraints added in 741.4 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... running ksdssp... Secondary structure from input PDB file: 13 helices and 0 sheets defined 84.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 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 125 through 156 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 177 removed outlier: 3.640A pdb=" N PHE A 166 " --> pdb=" O ILE A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 210 removed outlier: 3.716A pdb=" N MET A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 245 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 250 through 268 Processing helix chain 'A' and resid 285 through 289 Processing helix chain 'A' and resid 292 through 322 removed outlier: 4.157A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Proline residue: A 313 - end of helix Proline residue: A 316 - end of helix Processing helix chain 'A' and resid 329 through 355 removed outlier: 4.444A pdb=" N PHE A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Proline residue: A 336 - end of helix 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 357 through 377 Proline residue: A 376 - end of helix Processing helix chain 'A' and resid 381 through 413 removed outlier: 4.793A pdb=" N ALA A 386 " --> pdb=" O TYR A 382 " (cutoff:3.500A) Proline residue: A 387 - end of helix Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 418 through 446 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 449 through 469 Proline residue: A 465 - end of helix removed outlier: 4.898A pdb=" N PHE A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N PHE A 469 " --> pdb=" O PRO A 465 " (cutoff:3.500A) 223 hydrogen bonds defined for protein. 669 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: 0.80 Time building geometry restraints manager: 1.21 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: 749 2.81 - 3.33: 2982 3.33 - 3.85: 4808 3.85 - 4.38: 4984 4.38 - 4.90: 9160 Nonbonded interactions: 22683 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 22678 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: 1.420 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: 6.640 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.410 Find NCS groups from input model: 0.090 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.540 ------------------------------------------------------------------------------- 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= 0.246 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 : 0.338 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: 0.1378 time to fit residues: 7.8374 Evaluate side-chains 44 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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: 0.1980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 0.3980 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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: 0.7683 moved from start: 0.0701 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= 0.205 Angle : 0.653 9.563 4053 Z= 0.313 Chirality : 0.040 0.139 489 Planarity : 0.006 0.054 496 Dihedral : 5.528 34.150 416 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.65 % Allowed : 21.45 % 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: 2.33 (0.45), residues: 388 helix: 2.11 (0.30), residues: 328 sheet: None (None), residues: 0 loop : -1.77 (0.72), residues: 60 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 0.016 0.002 PHE A 27 TYR 0.010 0.001 TYR A 49 ARG 0.002 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 51 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.291 Fit side-chains REVERT: A 225 LEU cc_start: 0.7486 (mm) cc_final: 0.6496 (tt) REVERT: A 405 ILE cc_start: 0.8794 (mm) cc_final: 0.8564 (mt) REVERT: A 459 ILE cc_start: 0.7205 (mt) cc_final: 0.6935 (mm) outliers start: 5 outliers final: 3 residues processed: 50 average time/residue: 0.1237 time to fit residues: 7.9566 Evaluate side-chains 45 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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: 0.8980 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 38 optimal weight: 0.0870 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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: 0.7706 moved from start: 0.1041 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= 0.209 Angle : 0.647 9.563 4053 Z= 0.310 Chirality : 0.041 0.139 489 Planarity : 0.006 0.052 496 Dihedral : 4.779 19.253 416 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.30 % Allowed : 21.78 % Favored : 74.92 % 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: 2.32 (0.45), residues: 388 helix: 2.08 (0.30), residues: 331 sheet: None (None), residues: 0 loop : -1.80 (0.74), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 318 HIS 0.005 0.002 HIS A 53 PHE 0.015 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 53 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 0.324 Fit side-chains REVERT: A 196 SER cc_start: 0.8171 (t) cc_final: 0.7965 (p) REVERT: A 225 LEU cc_start: 0.7452 (mm) cc_final: 0.6444 (tt) REVERT: A 253 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6456 (mp) REVERT: A 405 ILE cc_start: 0.8829 (mm) cc_final: 0.8593 (mt) REVERT: A 459 ILE cc_start: 0.7215 (OUTLIER) cc_final: 0.6927 (mm) outliers start: 10 outliers final: 5 residues processed: 51 average time/residue: 0.1120 time to fit residues: 7.4269 Evaluate side-chains 47 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 385 ILE 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: 0.6980 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 0.4980 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 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 53 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2977 Z= 0.249 Angle : 0.660 9.403 4053 Z= 0.323 Chirality : 0.042 0.143 489 Planarity : 0.006 0.061 496 Dihedral : 4.661 18.484 416 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.96 % Allowed : 21.12 % Favored : 74.92 % 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: 2.22 (0.45), residues: 388 helix: 2.00 (0.30), residues: 330 sheet: None (None), residues: 0 loop : -1.66 (0.77), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 318 HIS 0.005 0.002 HIS A 53 PHE 0.014 0.002 PHE A 27 TYR 0.010 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 55 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 43 time to evaluate : 0.333 Fit side-chains REVERT: A 196 SER cc_start: 0.8126 (t) cc_final: 0.7912 (p) REVERT: A 225 LEU cc_start: 0.7560 (mm) cc_final: 0.6538 (tt) REVERT: A 253 LEU cc_start: 0.6770 (OUTLIER) cc_final: 0.6557 (mp) REVERT: A 405 ILE cc_start: 0.8793 (mm) cc_final: 0.8559 (mt) outliers start: 12 outliers final: 7 residues processed: 52 average time/residue: 0.1069 time to fit residues: 7.3346 Evaluate side-chains 50 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 375 ILE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 459 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 33 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS A 305 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2977 Z= 0.229 Angle : 0.643 9.393 4053 Z= 0.314 Chirality : 0.041 0.137 489 Planarity : 0.006 0.061 496 Dihedral : 4.602 18.771 416 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.96 % Allowed : 21.12 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.45), residues: 388 helix: 2.08 (0.30), residues: 330 sheet: None (None), residues: 0 loop : -1.66 (0.78), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 318 HIS 0.005 0.002 HIS A 53 PHE 0.014 0.002 PHE A 27 TYR 0.010 0.001 TYR A 49 ARG 0.001 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 56 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 44 time to evaluate : 0.315 Fit side-chains REVERT: A 196 SER cc_start: 0.8126 (t) cc_final: 0.7916 (p) REVERT: A 225 LEU cc_start: 0.7405 (mm) cc_final: 0.6453 (tt) REVERT: A 405 ILE cc_start: 0.8794 (mm) cc_final: 0.8567 (mt) REVERT: A 459 ILE cc_start: 0.7223 (OUTLIER) cc_final: 0.6934 (mm) outliers start: 12 outliers final: 6 residues processed: 53 average time/residue: 0.1072 time to fit residues: 7.5088 Evaluate side-chains 50 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 351 LEU Chi-restraints excluded: chain A residue 385 ILE 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: 1.9990 chunk 37 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 0.0670 chunk 36 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 27 optimal weight: 0.7980 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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: 0.7722 moved from start: 0.1784 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= 0.194 Angle : 0.637 9.495 4053 Z= 0.305 Chirality : 0.040 0.132 489 Planarity : 0.006 0.058 496 Dihedral : 4.456 17.996 416 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 5.28 % Allowed : 20.79 % 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: 2.45 (0.45), residues: 388 helix: 2.18 (0.30), residues: 331 sheet: None (None), residues: 0 loop : -1.90 (0.77), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 318 HIS 0.005 0.002 HIS A 53 PHE 0.014 0.001 PHE A 27 TYR 0.009 0.001 TYR A 49 ARG 0.002 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 63 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 47 time to evaluate : 0.308 Fit side-chains REVERT: A 225 LEU cc_start: 0.7388 (mm) cc_final: 0.6455 (tt) REVERT: A 397 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.7356 (mtm) REVERT: A 403 MET cc_start: 0.8451 (mmt) cc_final: 0.8248 (mmt) REVERT: A 405 ILE cc_start: 0.8753 (mm) cc_final: 0.8507 (mt) REVERT: A 459 ILE cc_start: 0.7218 (OUTLIER) cc_final: 0.6916 (mm) outliers start: 16 outliers final: 7 residues processed: 58 average time/residue: 0.1111 time to fit residues: 8.2950 Evaluate side-chains 53 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 375 ILE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 459 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.4980 chunk 31 optimal weight: 0.6980 chunk 37 optimal weight: 0.3980 chunk 23 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 0.2980 chunk 25 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS A 353 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1996 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= 0.190 Angle : 0.646 9.452 4053 Z= 0.309 Chirality : 0.040 0.131 489 Planarity : 0.006 0.054 496 Dihedral : 4.438 18.708 416 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.29 % Allowed : 23.43 % Favored : 72.28 % 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: 2.44 (0.45), residues: 388 helix: 2.20 (0.30), residues: 331 sheet: None (None), residues: 0 loop : -2.08 (0.72), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 318 HIS 0.004 0.001 HIS A 53 PHE 0.014 0.001 PHE A 27 TYR 0.008 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 58 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 45 time to evaluate : 0.314 Fit side-chains REVERT: A 52 LYS cc_start: 0.8156 (ttpt) cc_final: 0.7773 (ttpt) REVERT: A 225 LEU cc_start: 0.7267 (mm) cc_final: 0.6341 (tt) REVERT: A 397 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.7363 (mtm) REVERT: A 403 MET cc_start: 0.8434 (mmt) cc_final: 0.8228 (mmt) REVERT: A 405 ILE cc_start: 0.8757 (mm) cc_final: 0.8503 (mt) REVERT: A 459 ILE cc_start: 0.7220 (OUTLIER) cc_final: 0.6915 (mm) outliers start: 13 outliers final: 8 residues processed: 55 average time/residue: 0.1144 time to fit residues: 8.1906 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 ------------------------------------------------------------------------------- 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 385 ILE Chi-restraints excluded: chain A residue 397 MET 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: 1.9990 chunk 29 optimal weight: 0.0060 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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: 0.7727 moved from start: 0.2071 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= 0.203 Angle : 0.660 10.344 4053 Z= 0.314 Chirality : 0.040 0.132 489 Planarity : 0.006 0.058 496 Dihedral : 4.399 18.280 416 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.62 % Allowed : 24.42 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.45), residues: 388 helix: 2.18 (0.30), residues: 331 sheet: None (None), residues: 0 loop : -2.17 (0.71), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 318 HIS 0.004 0.001 HIS A 53 PHE 0.014 0.001 PHE A 27 TYR 0.009 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 59 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 45 time to evaluate : 0.311 Fit side-chains REVERT: A 225 LEU cc_start: 0.7251 (mm) cc_final: 0.6278 (tt) REVERT: A 397 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.7377 (mtm) REVERT: A 405 ILE cc_start: 0.8726 (mm) cc_final: 0.8476 (mt) REVERT: A 459 ILE cc_start: 0.7217 (OUTLIER) cc_final: 0.6905 (mm) outliers start: 14 outliers final: 6 residues processed: 56 average time/residue: 0.1143 time to fit residues: 8.2251 Evaluate side-chains 51 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 375 ILE Chi-restraints excluded: chain A residue 385 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: 6.9990 chunk 34 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 0.0370 chunk 38 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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: 0.7713 moved from start: 0.2186 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= 0.195 Angle : 0.668 10.903 4053 Z= 0.316 Chirality : 0.040 0.131 489 Planarity : 0.006 0.056 496 Dihedral : 4.388 18.534 416 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.97 % Allowed : 25.08 % Favored : 71.95 % 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: 2.44 (0.45), residues: 388 helix: 2.23 (0.30), residues: 330 sheet: None (None), residues: 0 loop : -2.18 (0.70), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 318 HIS 0.005 0.002 HIS A 53 PHE 0.014 0.001 PHE A 27 TYR 0.008 0.001 TYR A 49 ARG 0.001 0.000 ARG A 326 *********************** 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 55 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 46 time to evaluate : 0.319 Fit side-chains REVERT: A 225 LEU cc_start: 0.7165 (mm) cc_final: 0.6224 (tt) REVERT: A 397 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.7363 (mtm) REVERT: A 405 ILE cc_start: 0.8752 (mm) cc_final: 0.8497 (mt) REVERT: A 459 ILE cc_start: 0.7223 (OUTLIER) cc_final: 0.6911 (mm) outliers start: 9 outliers final: 6 residues processed: 52 average time/residue: 0.1124 time to fit residues: 7.5462 Evaluate side-chains 52 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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 375 ILE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 459 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 4 optimal weight: 0.0030 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 overall best weight: 0.5990 ------------------------------------------------------------------------------- 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: 0.7727 moved from start: 0.2244 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= 0.215 Angle : 0.683 10.699 4053 Z= 0.325 Chirality : 0.041 0.132 489 Planarity : 0.006 0.061 496 Dihedral : 4.402 18.340 416 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.97 % Allowed : 25.08 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.45), residues: 388 helix: 2.14 (0.30), residues: 331 sheet: None (None), residues: 0 loop : -2.17 (0.72), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 318 HIS 0.006 0.002 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 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 53 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.326 Fit side-chains REVERT: A 225 LEU cc_start: 0.7157 (mm) cc_final: 0.6217 (tt) REVERT: A 397 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.7395 (mtm) REVERT: A 405 ILE cc_start: 0.8735 (mm) cc_final: 0.8490 (mt) REVERT: A 459 ILE cc_start: 0.7240 (OUTLIER) cc_final: 0.6924 (mm) outliers start: 9 outliers final: 6 residues processed: 51 average time/residue: 0.1081 time to fit residues: 7.2613 Evaluate side-chains 52 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 375 ILE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 459 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.0970 chunk 15 optimal weight: 0.5980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.160350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.131149 restraints weight = 3680.902| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.46 r_work: 0.3472 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2977 Z= 0.223 Angle : 0.693 10.705 4053 Z= 0.328 Chirality : 0.041 0.133 489 Planarity : 0.006 0.060 496 Dihedral : 4.473 19.015 416 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.97 % Allowed : 25.41 % Favored : 71.62 % 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: 2.38 (0.45), residues: 388 helix: 2.16 (0.30), residues: 330 sheet: None (None), residues: 0 loop : -1.99 (0.73), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 318 HIS 0.005 0.002 HIS A 53 PHE 0.014 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: 1062.75 seconds wall clock time: 19 minutes 40.67 seconds (1180.67 seconds total)