Starting phenix.real_space_refine on Fri Dec 8 08:31:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0n_15789/12_2023/8b0n_15789_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0n_15789/12_2023/8b0n_15789.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0n_15789/12_2023/8b0n_15789_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0n_15789/12_2023/8b0n_15789_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0n_15789/12_2023/8b0n_15789_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0n_15789/12_2023/8b0n_15789.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0n_15789/12_2023/8b0n_15789.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0n_15789/12_2023/8b0n_15789_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0n_15789/12_2023/8b0n_15789_updated.pdb" } resolution = 2.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3852 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 15 5.16 5 C 2635 2.51 5 N 660 2.21 5 O 693 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 4004 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4004 Unusual residues: {'OU9': 1} Classifications: {'peptide': 510, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 36, 'TRANS': 473, None: 1} Not linked: pdbres="ARG A 510 " pdbres="OU9 A 601 " Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'P1L:plan-1': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 37 Time building chain proxies: 2.99, per 1000 atoms: 0.75 Number of scatterers: 4004 At special positions: 0 Unit cell: (59.472, 82.6, 85.904, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 P 1 15.00 O 693 8.00 N 660 7.00 C 2635 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: 2.09 Conformation dependent library (CDL) restraints added in 776.3 milliseconds 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 940 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 2 sheets defined 50.2% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 3 through 6 No H-bonds generated for 'chain 'A' and resid 3 through 6' Processing helix chain 'A' and resid 10 through 27 removed outlier: 3.560A pdb=" N GLY A 24 " --> pdb=" O PHE A 20 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THR A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ALA A 27 " --> pdb=" O CYS A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 46 removed outlier: 3.621A pdb=" N SER A 40 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 44 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN A 45 " --> pdb=" O MET A 42 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA A 46 " --> pdb=" O GLY A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 71 Processing helix chain 'A' and resid 73 through 80 Processing helix chain 'A' and resid 87 through 115 removed outlier: 4.257A pdb=" N TYR A 104 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 125 Processing helix chain 'A' and resid 127 through 139 Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 161 through 167 Proline residue: A 165 - end of helix Processing helix chain 'A' and resid 169 through 188 Processing helix chain 'A' and resid 192 through 210 Proline residue: A 205 - end of helix removed outlier: 4.864A pdb=" N LEU A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG A 209 " --> pdb=" O PRO A 205 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TYR A 210 " --> pdb=" O PHE A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 233 through 236 No H-bonds generated for 'chain 'A' and resid 233 through 236' Processing helix chain 'A' and resid 239 through 254 removed outlier: 4.389A pdb=" N LEU A 243 " --> pdb=" O GLU A 239 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 290 removed outlier: 3.777A pdb=" N GLN A 278 " --> pdb=" O ILE A 275 " (cutoff:3.500A) Proline residue: A 279 - end of helix removed outlier: 3.734A pdb=" N LYS A 282 " --> pdb=" O PRO A 279 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 283 " --> pdb=" O PHE A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 348 No H-bonds generated for 'chain 'A' and resid 346 through 348' Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'A' and resid 393 through 399 Processing helix chain 'A' and resid 420 through 436 removed outlier: 3.717A pdb=" N ARG A 432 " --> pdb=" O MET A 428 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A 433 " --> pdb=" O ALA A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 485 No H-bonds generated for 'chain 'A' and resid 482 through 485' Processing helix chain 'A' and resid 489 through 508 Processing sheet with id= A, first strand: chain 'A' and resid 468 through 474 removed outlier: 6.503A pdb=" N LEU A 262 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL A 227 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ILE A 264 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N SER A 294 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N TRP A 265 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL A 296 " --> pdb=" O TRP A 265 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 382 through 385 removed outlier: 7.275A pdb=" N TYR A 406 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N ALA A 385 " --> pdb=" O TYR A 406 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 408 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N THR A 409 " --> pdb=" O PRO A 439 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU A 441 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N SER A 411 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N SER A 443 " --> pdb=" O SER A 411 " (cutoff:3.500A) 170 hydrogen bonds defined for protein. 438 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: 1.12 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 612 1.31 - 1.43: 1141 1.43 - 1.56: 2333 1.56 - 1.68: 1 1.68 - 1.80: 29 Bond restraints: 4116 Sorted by residual: bond pdb=" N P1L A 387 " pdb=" CA P1L A 387 " ideal model delta sigma weight residual 1.442 1.489 -0.047 2.00e-02 2.50e+03 5.61e+00 bond pdb=" O11 OU9 A 601 " pdb=" P OU9 A 601 " ideal model delta sigma weight residual 1.648 1.695 -0.047 2.00e-02 2.50e+03 5.56e+00 bond pdb=" C P1L A 387 " pdb=" O P1L A 387 " ideal model delta sigma weight residual 1.234 1.188 0.046 2.00e-02 2.50e+03 5.35e+00 bond pdb=" SG P1L A 387 " pdb=" C7 P1L A 387 " ideal model delta sigma weight residual 1.733 1.691 0.042 2.00e-02 2.50e+03 4.40e+00 bond pdb=" C21 OU9 A 601 " pdb=" O21 OU9 A 601 " ideal model delta sigma weight residual 1.398 1.362 0.036 2.00e-02 2.50e+03 3.27e+00 ... (remaining 4111 not shown) Histogram of bond angle deviations from ideal: 100.34 - 107.08: 189 107.08 - 113.81: 2257 113.81 - 120.55: 1625 120.55 - 127.28: 1478 127.28 - 134.02: 68 Bond angle restraints: 5617 Sorted by residual: angle pdb=" O12 OU9 A 601 " pdb=" P OU9 A 601 " pdb=" O14 OU9 A 601 " ideal model delta sigma weight residual 109.47 126.39 -16.92 3.00e+00 1.11e-01 3.18e+01 angle pdb=" SG P1L A 387 " pdb=" C7 P1L A 387 " pdb=" C8 P1L A 387 " ideal model delta sigma weight residual 109.23 118.07 -8.84 3.00e+00 1.11e-01 8.68e+00 angle pdb=" C21 OU9 A 601 " pdb=" C22 OU9 A 601 " pdb=" C23 OU9 A 601 " ideal model delta sigma weight residual 109.47 117.51 -8.04 3.00e+00 1.11e-01 7.18e+00 angle pdb=" O11 OU9 A 601 " pdb=" P OU9 A 601 " pdb=" O13 OU9 A 601 " ideal model delta sigma weight residual 109.47 102.04 7.43 3.00e+00 1.11e-01 6.13e+00 angle pdb=" CA P1L A 387 " pdb=" C P1L A 387 " pdb=" O P1L A 387 " ideal model delta sigma weight residual 128.33 121.11 7.22 3.00e+00 1.11e-01 5.79e+00 ... (remaining 5612 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.37: 2293 16.37 - 32.74: 93 32.74 - 49.12: 15 49.12 - 65.49: 7 65.49 - 81.86: 4 Dihedral angle restraints: 2412 sinusoidal: 946 harmonic: 1466 Sorted by residual: dihedral pdb=" CA PHE A 28 " pdb=" C PHE A 28 " pdb=" N SER A 29 " pdb=" CA SER A 29 " ideal model delta harmonic sigma weight residual 180.00 -159.02 -20.98 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" C22 OU9 A 601 " pdb=" C23 OU9 A 601 " pdb=" C24 OU9 A 601 " pdb=" C25 OU9 A 601 " ideal model delta sinusoidal sigma weight residual 230.93 149.07 81.86 1 3.00e+01 1.11e-03 9.16e+00 dihedral pdb=" CB GLU A 435 " pdb=" CG GLU A 435 " pdb=" CD GLU A 435 " pdb=" OE1 GLU A 435 " ideal model delta sinusoidal sigma weight residual 0.00 77.85 -77.85 1 3.00e+01 1.11e-03 8.42e+00 ... (remaining 2409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 483 0.045 - 0.089: 101 0.089 - 0.134: 44 0.134 - 0.178: 2 0.178 - 0.223: 2 Chirality restraints: 632 Sorted by residual: chirality pdb=" CA P1L A 387 " pdb=" N P1L A 387 " pdb=" C P1L A 387 " pdb=" CB P1L A 387 " both_signs ideal model delta sigma weight residual False 2.27 2.49 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" C2 OU9 A 601 " pdb=" C1 OU9 A 601 " pdb=" C3 OU9 A 601 " pdb=" O21 OU9 A 601 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA TRP A 489 " pdb=" N TRP A 489 " pdb=" C TRP A 489 " pdb=" CB TRP A 489 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.95e-01 ... (remaining 629 not shown) Planarity restraints: 705 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 87 " 0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO A 88 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 88 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 88 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 34 " -0.022 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO A 35 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 35 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 35 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 204 " -0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO A 205 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 205 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 205 " -0.016 5.00e-02 4.00e+02 ... (remaining 702 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 973 2.79 - 3.32: 4020 3.32 - 3.85: 7005 3.85 - 4.37: 8797 4.37 - 4.90: 14580 Nonbonded interactions: 35375 Sorted by model distance: nonbonded pdb=" OH TYR A 333 " pdb=" OE1 GLU A 389 " model vdw 2.267 2.440 nonbonded pdb=" O PHE A 151 " pdb=" OG SER A 154 " model vdw 2.290 2.440 nonbonded pdb=" OG SER A 225 " pdb=" OG SER A 260 " model vdw 2.298 2.440 nonbonded pdb=" O GLY A 229 " pdb=" NH1 ARG A 467 " model vdw 2.300 2.520 nonbonded pdb=" O PRO A 361 " pdb=" N OU9 A 601 " model vdw 2.332 2.520 ... (remaining 35370 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: 0.000 Extract box with map and model: 3.140 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.160 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:13.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 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 0.047 4116 Z= 0.237 Angle : 0.660 16.922 5617 Z= 0.278 Chirality : 0.044 0.223 632 Planarity : 0.004 0.037 705 Dihedral : 10.562 81.859 1472 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.38), residues: 505 helix: 1.01 (0.34), residues: 235 sheet: 0.49 (0.59), residues: 68 loop : 0.05 (0.48), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 489 HIS 0.001 0.001 HIS A 425 PHE 0.008 0.001 PHE A 426 TYR 0.009 0.001 TYR A 406 ARG 0.002 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.509 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 1.0919 time to fit residues: 63.7127 Evaluate side-chains 46 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.413 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 0.0040 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN A 244 ASN A 488 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4116 Z= 0.183 Angle : 0.534 5.920 5617 Z= 0.262 Chirality : 0.043 0.167 632 Planarity : 0.005 0.038 705 Dihedral : 8.853 81.593 585 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.74 % Allowed : 6.13 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.38), residues: 505 helix: 1.08 (0.34), residues: 235 sheet: 0.29 (0.57), residues: 68 loop : 0.12 (0.49), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 492 HIS 0.002 0.001 HIS A 425 PHE 0.013 0.001 PHE A 174 TYR 0.009 0.001 TYR A 406 ARG 0.008 0.001 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.424 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 53 average time/residue: 1.0114 time to fit residues: 56.0422 Evaluate side-chains 48 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.451 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.6102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN A 244 ASN ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4116 Z= 0.248 Angle : 0.535 5.999 5617 Z= 0.263 Chirality : 0.044 0.174 632 Planarity : 0.005 0.036 705 Dihedral : 7.759 63.333 585 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.47 % Allowed : 7.60 % Favored : 90.93 % 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: 0.66 (0.38), residues: 505 helix: 0.92 (0.33), residues: 241 sheet: 0.25 (0.57), residues: 68 loop : 0.08 (0.50), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 489 HIS 0.001 0.001 HIS A 425 PHE 0.013 0.001 PHE A 174 TYR 0.009 0.001 TYR A 325 ARG 0.005 0.000 ARG A 9 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.461 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 47 average time/residue: 1.1398 time to fit residues: 55.9689 Evaluate side-chains 45 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 0.457 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.0399 time to fit residues: 0.6862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 34 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN A 244 ASN ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4116 Z= 0.215 Angle : 0.526 5.963 5617 Z= 0.257 Chirality : 0.043 0.168 632 Planarity : 0.004 0.036 705 Dihedral : 7.493 62.813 585 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.74 % Allowed : 8.09 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.38), residues: 505 helix: 0.98 (0.33), residues: 241 sheet: 0.29 (0.57), residues: 68 loop : 0.05 (0.49), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 489 HIS 0.001 0.001 HIS A 425 PHE 0.013 0.001 PHE A 174 TYR 0.009 0.001 TYR A 325 ARG 0.006 0.000 ARG A 9 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.457 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 45 average time/residue: 1.0613 time to fit residues: 50.0325 Evaluate side-chains 45 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 0.510 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.6691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 0 optimal weight: 8.9990 chunk 36 optimal weight: 0.5980 chunk 20 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 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 241 GLN A 244 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4116 Z= 0.178 Angle : 0.517 5.908 5617 Z= 0.251 Chirality : 0.042 0.162 632 Planarity : 0.004 0.036 705 Dihedral : 7.252 60.179 585 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.98 % Allowed : 8.82 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.39), residues: 505 helix: 1.08 (0.34), residues: 241 sheet: 0.29 (0.57), residues: 68 loop : 0.05 (0.50), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 489 HIS 0.001 0.000 HIS A 337 PHE 0.012 0.001 PHE A 174 TYR 0.009 0.001 TYR A 406 ARG 0.007 0.000 ARG A 9 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.448 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 44 average time/residue: 1.0853 time to fit residues: 49.9086 Evaluate side-chains 43 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.465 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.6045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 12 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 28 optimal weight: 0.0980 chunk 36 optimal weight: 0.4980 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 241 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4116 Z= 0.186 Angle : 0.514 5.917 5617 Z= 0.251 Chirality : 0.043 0.165 632 Planarity : 0.004 0.037 705 Dihedral : 7.149 58.583 585 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.74 % Allowed : 9.07 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.38), residues: 505 helix: 1.12 (0.34), residues: 241 sheet: 0.31 (0.57), residues: 68 loop : 0.03 (0.49), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 489 HIS 0.001 0.000 HIS A 337 PHE 0.012 0.001 PHE A 174 TYR 0.008 0.001 TYR A 406 ARG 0.006 0.000 ARG A 9 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.477 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 43 average time/residue: 1.0547 time to fit residues: 47.5239 Evaluate side-chains 41 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.441 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.5997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 30 optimal weight: 0.4980 chunk 29 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 0.0770 overall best weight: 1.1144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4116 Z= 0.248 Angle : 0.536 5.983 5617 Z= 0.263 Chirality : 0.044 0.175 632 Planarity : 0.004 0.037 705 Dihedral : 7.282 58.302 585 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.49 % Allowed : 9.80 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.38), residues: 505 helix: 0.98 (0.33), residues: 240 sheet: 0.30 (0.57), residues: 67 loop : 0.07 (0.49), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 489 HIS 0.001 0.000 HIS A 425 PHE 0.013 0.001 PHE A 174 TYR 0.009 0.001 TYR A 104 ARG 0.006 0.000 ARG A 9 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.451 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 41 average time/residue: 1.1318 time to fit residues: 48.4838 Evaluate side-chains 39 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.447 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.5878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 0.0050 chunk 14 optimal weight: 0.0030 overall best weight: 0.5406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4116 Z= 0.166 Angle : 0.507 5.851 5617 Z= 0.248 Chirality : 0.042 0.156 632 Planarity : 0.004 0.037 705 Dihedral : 6.948 56.994 585 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.49 % Allowed : 9.31 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.38), residues: 505 helix: 1.14 (0.34), residues: 241 sheet: 0.45 (0.58), residues: 63 loop : -0.04 (0.48), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 489 HIS 0.001 0.000 HIS A 337 PHE 0.012 0.001 PHE A 174 TYR 0.009 0.001 TYR A 406 ARG 0.006 0.000 ARG A 9 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.358 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 39 average time/residue: 1.1611 time to fit residues: 47.1866 Evaluate side-chains 40 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.438 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.5922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 2.9990 chunk 43 optimal weight: 0.0050 chunk 45 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 40 optimal weight: 0.0570 overall best weight: 0.5914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4116 Z= 0.173 Angle : 0.508 5.891 5617 Z= 0.249 Chirality : 0.042 0.160 632 Planarity : 0.004 0.037 705 Dihedral : 6.735 55.522 585 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.49 % Allowed : 9.80 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.39), residues: 505 helix: 1.16 (0.34), residues: 241 sheet: 0.37 (0.57), residues: 68 loop : -0.02 (0.49), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 489 HIS 0.001 0.000 HIS A 337 PHE 0.012 0.001 PHE A 174 TYR 0.009 0.001 TYR A 313 ARG 0.007 0.000 ARG A 9 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.398 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 41 average time/residue: 1.1939 time to fit residues: 50.9598 Evaluate side-chains 39 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.448 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.6204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 4 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 43 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 37 optimal weight: 0.0070 chunk 5 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4116 Z= 0.166 Angle : 0.514 5.867 5617 Z= 0.249 Chirality : 0.042 0.157 632 Planarity : 0.004 0.037 705 Dihedral : 6.532 54.244 585 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.74 % Allowed : 9.56 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.39), residues: 505 helix: 1.20 (0.34), residues: 241 sheet: 0.36 (0.57), residues: 68 loop : -0.01 (0.49), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 489 HIS 0.001 0.000 HIS A 337 PHE 0.012 0.001 PHE A 174 TYR 0.008 0.001 TYR A 406 ARG 0.007 0.000 ARG A 9 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.453 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 43 average time/residue: 1.1556 time to fit residues: 51.8743 Evaluate side-chains 42 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.484 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.6433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 1 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.120615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.086982 restraints weight = 4742.668| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.11 r_work: 0.2806 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4116 Z= 0.182 Angle : 0.521 5.891 5617 Z= 0.253 Chirality : 0.042 0.160 632 Planarity : 0.004 0.037 705 Dihedral : 6.432 53.663 585 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.49 % Allowed : 10.05 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.39), residues: 505 helix: 1.19 (0.34), residues: 241 sheet: 0.34 (0.57), residues: 68 loop : -0.01 (0.49), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 489 HIS 0.001 0.000 HIS A 337 PHE 0.012 0.001 PHE A 174 TYR 0.008 0.001 TYR A 406 ARG 0.007 0.000 ARG A 9 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1796.10 seconds wall clock time: 32 minutes 59.65 seconds (1979.65 seconds total)