Starting phenix.real_space_refine on Wed Mar 5 18:39:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jtt_36652/03_2025/8jtt_36652.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jtt_36652/03_2025/8jtt_36652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jtt_36652/03_2025/8jtt_36652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jtt_36652/03_2025/8jtt_36652.map" model { file = "/net/cci-nas-00/data/ceres_data/8jtt_36652/03_2025/8jtt_36652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jtt_36652/03_2025/8jtt_36652.cif" } resolution = 3.87 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= 0.083 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 21 5.16 5 C 2182 2.51 5 N 534 2.21 5 O 584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3321 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3312 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 20, 'TRANS': 433} Chain breaks: 1 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 197 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 113 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'MF8': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.49, per 1000 atoms: 0.75 Number of scatterers: 3321 At special positions: 0 Unit cell: (85.5175, 58.455, 64.95, 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 21 16.00 O 584 8.00 N 534 7.00 C 2182 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 386.0 milliseconds 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 836 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 0 sheets defined 78.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 4 through 11 Processing helix chain 'A' and resid 15 through 30 Processing helix chain 'A' and resid 32 through 37 removed outlier: 4.023A pdb=" N CYS A 36 " --> pdb=" O PHE A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 42 Processing helix chain 'A' and resid 133 through 138 Processing helix chain 'A' and resid 143 through 173 removed outlier: 3.515A pdb=" N LEU A 148 " --> pdb=" O ASP A 144 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 150 " --> pdb=" O TRP A 146 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASP A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 195 removed outlier: 3.724A pdb=" N PHE A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 228 Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 232 through 255 removed outlier: 3.704A pdb=" N VAL A 236 " --> pdb=" O SER A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 278 removed outlier: 3.907A pdb=" N LEU A 264 " --> pdb=" O HIS A 260 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Proline residue: A 271 - end of helix Processing helix chain 'A' and resid 285 through 291 Processing helix chain 'A' and resid 294 through 310 Processing helix chain 'A' and resid 320 through 324 removed outlier: 3.794A pdb=" N GLU A 323 " --> pdb=" O LEU A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 338 removed outlier: 4.146A pdb=" N LEU A 337 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A 338 " --> pdb=" O ALA A 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 334 through 338' Processing helix chain 'A' and resid 339 through 367 removed outlier: 5.596A pdb=" N LYS A 345 " --> pdb=" O PRO A 341 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ARG A 346 " --> pdb=" O ARG A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 384 Processing helix chain 'A' and resid 385 through 397 removed outlier: 3.749A pdb=" N GLY A 389 " --> pdb=" O VAL A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 418 Processing helix chain 'A' and resid 419 through 422 Processing helix chain 'A' and resid 429 through 456 removed outlier: 3.702A pdb=" N CYS A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 451 " --> pdb=" O GLN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 470 Processing helix chain 'A' and resid 473 through 491 Proline residue: A 481 - end of helix Processing helix chain 'A' and resid 492 through 510 removed outlier: 3.962A pdb=" N LEU A 496 " --> pdb=" O GLN A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 530 removed outlier: 3.917A pdb=" N ALA A 528 " --> pdb=" O THR A 524 " (cutoff:3.500A) 236 hydrogen bonds defined for protein. 696 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: 0.82 Time building geometry restraints manager: 0.90 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: 1031 1.34 - 1.46: 712 1.46 - 1.58: 1625 1.58 - 1.69: 0 1.69 - 1.81: 32 Bond restraints: 3400 Sorted by residual: bond pdb=" C07 MF8 A 601 " pdb=" N08 MF8 A 601 " ideal model delta sigma weight residual 1.281 1.439 -0.158 2.00e-02 2.50e+03 6.28e+01 bond pdb=" C07 MF8 A 601 " pdb=" N06 MF8 A 601 " ideal model delta sigma weight residual 1.393 1.252 0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" C04 MF8 A 601 " pdb=" N02 MF8 A 601 " ideal model delta sigma weight residual 1.362 1.448 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" C07 MF8 A 601 " pdb=" N09 MF8 A 601 " ideal model delta sigma weight residual 1.358 1.444 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C04 MF8 A 601 " pdb=" N06 MF8 A 601 " ideal model delta sigma weight residual 1.387 1.454 -0.067 2.00e-02 2.50e+03 1.11e+01 ... (remaining 3395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 4470 1.92 - 3.85: 157 3.85 - 5.77: 19 5.77 - 7.69: 12 7.69 - 9.62: 3 Bond angle restraints: 4661 Sorted by residual: angle pdb=" N02 MF8 A 601 " pdb=" C04 MF8 A 601 " pdb=" N05 MF8 A 601 " ideal model delta sigma weight residual 126.24 116.62 9.62 3.00e+00 1.11e-01 1.03e+01 angle pdb=" N02 MF8 A 601 " pdb=" C04 MF8 A 601 " pdb=" N06 MF8 A 601 " ideal model delta sigma weight residual 113.43 122.89 -9.46 3.00e+00 1.11e-01 9.93e+00 angle pdb=" N ARG A 439 " pdb=" CA ARG A 439 " pdb=" C ARG A 439 " ideal model delta sigma weight residual 111.07 107.88 3.19 1.07e+00 8.73e-01 8.88e+00 angle pdb=" N MET A 448 " pdb=" CA MET A 448 " pdb=" C MET A 448 " ideal model delta sigma weight residual 111.14 113.92 -2.78 1.08e+00 8.57e-01 6.62e+00 angle pdb=" C VAL A 212 " pdb=" CA VAL A 212 " pdb=" CB VAL A 212 " ideal model delta sigma weight residual 112.22 108.70 3.52 1.38e+00 5.25e-01 6.52e+00 ... (remaining 4656 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.55: 1766 16.55 - 33.10: 150 33.10 - 49.65: 31 49.65 - 66.20: 0 66.20 - 82.75: 1 Dihedral angle restraints: 1948 sinusoidal: 648 harmonic: 1300 Sorted by residual: dihedral pdb=" CA THR A 396 " pdb=" C THR A 396 " pdb=" N ILE A 397 " pdb=" CA ILE A 397 " ideal model delta harmonic sigma weight residual -180.00 -161.54 -18.46 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA LEU A 521 " pdb=" C LEU A 521 " pdb=" N PRO A 522 " pdb=" CA PRO A 522 " ideal model delta harmonic sigma weight residual 180.00 164.07 15.93 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA LEU A 27 " pdb=" C LEU A 27 " pdb=" N LEU A 28 " pdb=" CA LEU A 28 " ideal model delta harmonic sigma weight residual 180.00 164.52 15.48 0 5.00e+00 4.00e-02 9.59e+00 ... (remaining 1945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 414 0.048 - 0.097: 116 0.097 - 0.145: 29 0.145 - 0.193: 2 0.193 - 0.241: 4 Chirality restraints: 565 Sorted by residual: chirality pdb=" CB THR A 45 " pdb=" CA THR A 45 " pdb=" OG1 THR A 45 " pdb=" CG2 THR A 45 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB VAL A 228 " pdb=" CA VAL A 228 " pdb=" CG1 VAL A 228 " pdb=" CG2 VAL A 228 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB VAL A 166 " pdb=" CA VAL A 166 " pdb=" CG1 VAL A 166 " pdb=" CG2 VAL A 166 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.52e-01 ... (remaining 562 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C01 MF8 A 601 " -0.222 2.00e-02 2.50e+03 3.51e-01 2.78e+03 pdb=" C03 MF8 A 601 " -0.138 2.00e-02 2.50e+03 pdb=" C04 MF8 A 601 " 0.229 2.00e-02 2.50e+03 pdb=" C07 MF8 A 601 " -0.097 2.00e-02 2.50e+03 pdb=" N02 MF8 A 601 " -0.043 2.00e-02 2.50e+03 pdb=" N05 MF8 A 601 " 0.587 2.00e-02 2.50e+03 pdb=" N06 MF8 A 601 " 0.083 2.00e-02 2.50e+03 pdb=" N08 MF8 A 601 " 0.325 2.00e-02 2.50e+03 pdb=" N09 MF8 A 601 " -0.723 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 270 " -0.039 5.00e-02 4.00e+02 5.85e-02 5.48e+00 pdb=" N PRO A 271 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 282 " -0.032 5.00e-02 4.00e+02 4.86e-02 3.77e+00 pdb=" N PRO A 283 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 283 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 283 " -0.027 5.00e-02 4.00e+02 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 752 2.78 - 3.31: 3285 3.31 - 3.84: 5585 3.84 - 4.37: 5758 4.37 - 4.90: 9929 Nonbonded interactions: 25309 Sorted by model distance: nonbonded pdb=" OG SER A 409 " pdb=" O GLY A 441 " model vdw 2.250 3.040 nonbonded pdb=" O PHE A 22 " pdb=" OH TYR A 240 " model vdw 2.252 3.040 nonbonded pdb=" O LEU A 42 " pdb=" OG SER A 133 " model vdw 2.348 3.040 nonbonded pdb=" OG1 THR A 245 " pdb=" OE1 GLU A 386 " model vdw 2.357 3.040 nonbonded pdb=" OG SER A 189 " pdb=" OE1 GLN A 209 " model vdw 2.391 3.040 ... (remaining 25304 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.050 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5705 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 : 0.006 0.158 3400 Z= 0.400 Angle : 0.869 9.617 4661 Z= 0.444 Chirality : 0.049 0.241 565 Planarity : 0.016 0.351 581 Dihedral : 12.926 82.753 1112 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.35), residues: 450 helix: -0.51 (0.26), residues: 327 sheet: None (None), residues: 0 loop : -3.46 (0.45), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 217 HIS 0.002 0.001 HIS A 367 PHE 0.027 0.002 PHE A 482 TYR 0.015 0.001 TYR A 240 ARG 0.002 0.000 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.339 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1027 time to fit residues: 9.9410 Evaluate side-chains 54 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 0.2980 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5401 r_free = 0.5401 target = 0.298009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5159 r_free = 0.5159 target = 0.267618 restraints weight = 3847.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.5203 r_free = 0.5203 target = 0.273787 restraints weight = 2234.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.5224 r_free = 0.5224 target = 0.277361 restraints weight = 1521.839| |-----------------------------------------------------------------------------| r_work (final): 0.5227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5829 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3400 Z= 0.190 Angle : 0.594 10.202 4661 Z= 0.304 Chirality : 0.039 0.133 565 Planarity : 0.005 0.049 581 Dihedral : 4.364 16.426 475 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.15 % Allowed : 7.38 % Favored : 90.46 % 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: -0.85 (0.39), residues: 450 helix: 0.35 (0.28), residues: 330 sheet: None (None), residues: 0 loop : -3.13 (0.52), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 261 HIS 0.003 0.001 HIS A 260 PHE 0.009 0.001 PHE A 22 TYR 0.010 0.001 TYR A 199 ARG 0.002 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.307 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 60 average time/residue: 0.0898 time to fit residues: 7.5954 Evaluate side-chains 58 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 385 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 22 optimal weight: 10.0000 chunk 20 optimal weight: 0.1980 chunk 27 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5506 r_free = 0.5506 target = 0.308133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.5262 r_free = 0.5262 target = 0.279786 restraints weight = 3734.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.5301 r_free = 0.5301 target = 0.285316 restraints weight = 2255.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.5316 r_free = 0.5316 target = 0.287530 restraints weight = 1584.928| |-----------------------------------------------------------------------------| r_work (final): 0.5351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5893 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3400 Z= 0.173 Angle : 0.560 9.430 4661 Z= 0.284 Chirality : 0.038 0.142 565 Planarity : 0.004 0.046 581 Dihedral : 4.135 14.981 475 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.46 % Allowed : 13.23 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.40), residues: 450 helix: 0.66 (0.28), residues: 334 sheet: None (None), residues: 0 loop : -3.12 (0.53), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 261 HIS 0.002 0.001 HIS A 260 PHE 0.010 0.001 PHE A 22 TYR 0.008 0.001 TYR A 240 ARG 0.002 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.358 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 60 average time/residue: 0.0930 time to fit residues: 7.7939 Evaluate side-chains 60 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 442 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 1 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5462 r_free = 0.5462 target = 0.302375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5206 r_free = 0.5206 target = 0.272948 restraints weight = 3825.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.5245 r_free = 0.5245 target = 0.278561 restraints weight = 2351.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.5264 r_free = 0.5264 target = 0.281644 restraints weight = 1657.285| |-----------------------------------------------------------------------------| r_work (final): 0.5201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5973 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3400 Z= 0.211 Angle : 0.587 9.156 4661 Z= 0.302 Chirality : 0.038 0.146 565 Planarity : 0.004 0.046 581 Dihedral : 4.232 14.883 475 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.00 % Allowed : 16.00 % Favored : 80.00 % 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: -0.30 (0.40), residues: 450 helix: 0.78 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -2.85 (0.53), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 261 HIS 0.004 0.001 HIS A 260 PHE 0.024 0.002 PHE A 151 TYR 0.009 0.001 TYR A 240 ARG 0.002 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.312 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 70 average time/residue: 0.0863 time to fit residues: 8.4547 Evaluate side-chains 64 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 29 optimal weight: 0.0980 chunk 3 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 6 optimal weight: 0.0470 chunk 9 optimal weight: 0.4980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5408 r_free = 0.5408 target = 0.298492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5200 r_free = 0.5200 target = 0.271659 restraints weight = 3915.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.5225 r_free = 0.5225 target = 0.276001 restraints weight = 2279.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.5256 r_free = 0.5256 target = 0.280485 restraints weight = 1628.735| |-----------------------------------------------------------------------------| r_work (final): 0.5268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5894 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3400 Z= 0.166 Angle : 0.550 9.174 4661 Z= 0.278 Chirality : 0.037 0.134 565 Planarity : 0.004 0.046 581 Dihedral : 4.038 15.335 475 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.46 % Allowed : 20.00 % Favored : 77.54 % 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: -0.05 (0.41), residues: 450 helix: 0.94 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -2.73 (0.54), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 261 HIS 0.001 0.001 HIS A 260 PHE 0.016 0.001 PHE A 275 TYR 0.006 0.001 TYR A 199 ARG 0.001 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.309 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 65 average time/residue: 0.0839 time to fit residues: 7.6899 Evaluate side-chains 63 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 2.9990 chunk 23 optimal weight: 0.0040 chunk 44 optimal weight: 0.0770 chunk 2 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 overall best weight: 0.5550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5399 r_free = 0.5399 target = 0.297217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.5178 r_free = 0.5178 target = 0.269651 restraints weight = 3989.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.5221 r_free = 0.5221 target = 0.275461 restraints weight = 2380.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.5237 r_free = 0.5237 target = 0.278626 restraints weight = 1636.837| |-----------------------------------------------------------------------------| r_work (final): 0.5244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5918 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3400 Z= 0.180 Angle : 0.567 8.950 4661 Z= 0.283 Chirality : 0.037 0.126 565 Planarity : 0.004 0.046 581 Dihedral : 4.036 16.127 475 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.85 % Allowed : 20.92 % Favored : 77.23 % 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: -0.00 (0.40), residues: 450 helix: 0.98 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -2.74 (0.53), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 261 HIS 0.001 0.001 HIS A 260 PHE 0.027 0.001 PHE A 151 TYR 0.005 0.001 TYR A 199 ARG 0.001 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.308 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 62 average time/residue: 0.0911 time to fit residues: 7.9705 Evaluate side-chains 63 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 442 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 38 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 20 optimal weight: 0.4980 chunk 41 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5458 r_free = 0.5458 target = 0.301919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.5214 r_free = 0.5214 target = 0.273442 restraints weight = 3819.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.5255 r_free = 0.5255 target = 0.279166 restraints weight = 2285.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.5273 r_free = 0.5273 target = 0.282307 restraints weight = 1582.765| |-----------------------------------------------------------------------------| r_work (final): 0.5235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5966 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3400 Z= 0.192 Angle : 0.576 8.979 4661 Z= 0.291 Chirality : 0.038 0.127 565 Planarity : 0.004 0.046 581 Dihedral : 4.025 15.216 475 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.77 % Allowed : 21.23 % Favored : 76.00 % 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: -0.05 (0.41), residues: 450 helix: 0.90 (0.29), residues: 329 sheet: None (None), residues: 0 loop : -2.65 (0.56), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 261 HIS 0.002 0.001 HIS A 367 PHE 0.014 0.001 PHE A 499 TYR 0.006 0.001 TYR A 240 ARG 0.001 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.305 Fit side-chains REVERT: A 173 PHE cc_start: 0.4562 (OUTLIER) cc_final: 0.4081 (m-10) outliers start: 9 outliers final: 8 residues processed: 65 average time/residue: 0.0957 time to fit residues: 8.5028 Evaluate side-chains 66 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 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 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5236 r_free = 0.5236 target = 0.280338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.5021 r_free = 0.5021 target = 0.252602 restraints weight = 3965.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.5053 r_free = 0.5053 target = 0.257782 restraints weight = 2354.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.5093 r_free = 0.5093 target = 0.261840 restraints weight = 1627.092| |-----------------------------------------------------------------------------| r_work (final): 0.5218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5962 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3400 Z= 0.199 Angle : 0.591 8.831 4661 Z= 0.300 Chirality : 0.038 0.139 565 Planarity : 0.004 0.046 581 Dihedral : 4.073 15.465 475 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.38 % Allowed : 22.46 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.41), residues: 450 helix: 0.89 (0.29), residues: 329 sheet: None (None), residues: 0 loop : -2.64 (0.55), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 261 HIS 0.002 0.001 HIS A 367 PHE 0.030 0.001 PHE A 151 TYR 0.006 0.001 TYR A 199 ARG 0.002 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.341 Fit side-chains REVERT: A 173 PHE cc_start: 0.4562 (OUTLIER) cc_final: 0.4139 (m-10) outliers start: 11 outliers final: 9 residues processed: 65 average time/residue: 0.0961 time to fit residues: 8.6921 Evaluate side-chains 67 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 22 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 43 optimal weight: 0.0270 chunk 44 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5453 r_free = 0.5453 target = 0.301350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.5211 r_free = 0.5211 target = 0.272701 restraints weight = 3831.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.5241 r_free = 0.5241 target = 0.277804 restraints weight = 2273.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.5282 r_free = 0.5282 target = 0.282140 restraints weight = 1599.587| |-----------------------------------------------------------------------------| r_work (final): 0.5310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5989 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3400 Z= 0.198 Angle : 0.584 8.807 4661 Z= 0.296 Chirality : 0.038 0.134 565 Planarity : 0.004 0.046 581 Dihedral : 4.081 15.266 475 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.08 % Allowed : 24.31 % Favored : 72.62 % 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: -0.05 (0.41), residues: 450 helix: 0.88 (0.29), residues: 329 sheet: None (None), residues: 0 loop : -2.59 (0.56), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 261 HIS 0.002 0.001 HIS A 367 PHE 0.029 0.002 PHE A 151 TYR 0.006 0.001 TYR A 199 ARG 0.002 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.317 Fit side-chains REVERT: A 173 PHE cc_start: 0.4673 (OUTLIER) cc_final: 0.4196 (m-10) outliers start: 10 outliers final: 9 residues processed: 63 average time/residue: 0.0910 time to fit residues: 8.1584 Evaluate side-chains 65 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 442 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 17 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 20 optimal weight: 0.0030 chunk 41 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 4 optimal weight: 0.0050 chunk 44 optimal weight: 0.9980 overall best weight: 0.4804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5397 r_free = 0.5397 target = 0.296879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5194 r_free = 0.5194 target = 0.271229 restraints weight = 3894.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.5219 r_free = 0.5219 target = 0.276035 restraints weight = 2268.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.5257 r_free = 0.5257 target = 0.280026 restraints weight = 1586.033| |-----------------------------------------------------------------------------| r_work (final): 0.5349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5913 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3400 Z= 0.181 Angle : 0.570 8.942 4661 Z= 0.286 Chirality : 0.037 0.118 565 Planarity : 0.004 0.046 581 Dihedral : 3.981 15.404 475 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.46 % Allowed : 25.23 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.41), residues: 450 helix: 1.04 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -2.60 (0.55), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 261 HIS 0.002 0.001 HIS A 367 PHE 0.009 0.001 PHE A 275 TYR 0.005 0.001 TYR A 199 ARG 0.001 0.000 ARG A 439 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.339 Fit side-chains REVERT: A 173 PHE cc_start: 0.4456 (OUTLIER) cc_final: 0.3954 (m-10) outliers start: 8 outliers final: 7 residues processed: 63 average time/residue: 0.0886 time to fit residues: 7.8251 Evaluate side-chains 63 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 442 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 23 optimal weight: 10.0000 chunk 41 optimal weight: 0.0770 chunk 2 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5388 r_free = 0.5388 target = 0.295204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.5170 r_free = 0.5170 target = 0.268424 restraints weight = 3907.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.5216 r_free = 0.5216 target = 0.274000 restraints weight = 2308.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.5233 r_free = 0.5233 target = 0.277090 restraints weight = 1592.297| |-----------------------------------------------------------------------------| r_work (final): 0.5342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5989 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3400 Z= 0.194 Angle : 0.590 8.867 4661 Z= 0.296 Chirality : 0.038 0.128 565 Planarity : 0.004 0.046 581 Dihedral : 3.995 15.362 475 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.46 % Allowed : 25.54 % Favored : 72.00 % 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: 0.11 (0.41), residues: 450 helix: 1.01 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -2.56 (0.56), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 261 HIS 0.002 0.001 HIS A 367 PHE 0.010 0.001 PHE A 499 TYR 0.007 0.001 TYR A 240 ARG 0.001 0.000 ARG A 439 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1257.47 seconds wall clock time: 22 minutes 25.56 seconds (1345.56 seconds total)