Starting phenix.real_space_refine on Mon Jan 13 19:13:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f6q_50238/01_2025/9f6q_50238.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f6q_50238/01_2025/9f6q_50238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9f6q_50238/01_2025/9f6q_50238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f6q_50238/01_2025/9f6q_50238.map" model { file = "/net/cci-nas-00/data/ceres_data/9f6q_50238/01_2025/9f6q_50238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f6q_50238/01_2025/9f6q_50238.cif" } resolution = 3.9 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= 0.022 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 22 5.16 5 C 2392 2.51 5 N 589 2.21 5 O 615 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 3618 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3618 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 19, 'TRANS': 449} Time building chain proxies: 2.69, per 1000 atoms: 0.74 Number of scatterers: 3618 At special positions: 0 Unit cell: (84.63, 69.006, 71.61, 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 22 16.00 O 615 8.00 N 589 7.00 C 2392 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 233 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 354 " distance=2.03 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: 0.98 Conformation dependent library (CDL) restraints added in 436.1 milliseconds 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 864 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 0 sheets defined 87.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 54 through 62 Processing helix chain 'A' and resid 63 through 73 removed outlier: 3.887A pdb=" N LEU A 67 " --> pdb=" O GLY A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 88 Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 92 through 118 Processing helix chain 'A' and resid 120 through 129 Processing helix chain 'A' and resid 130 through 165 Processing helix chain 'A' and resid 169 through 187 Processing helix chain 'A' and resid 188 through 191 removed outlier: 3.747A pdb=" N GLY A 191 " --> pdb=" O ASP A 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 188 through 191' Processing helix chain 'A' and resid 195 through 218 Processing helix chain 'A' and resid 220 through 230 removed outlier: 4.182A pdb=" N LEU A 224 " --> pdb=" O GLU A 220 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 252 removed outlier: 3.733A pdb=" N ILE A 252 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 264 removed outlier: 4.517A pdb=" N TYR A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 273 through 311 removed outlier: 3.525A pdb=" N ILE A 277 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 322 Processing helix chain 'A' and resid 344 through 357 Processing helix chain 'A' and resid 357 through 391 removed outlier: 3.756A pdb=" N LEU A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 419 Proline residue: A 411 - end of helix Processing helix chain 'A' and resid 420 through 439 Processing helix chain 'A' and resid 439 through 452 Proline residue: A 445 - end of helix removed outlier: 3.557A pdb=" N MET A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 488 Processing helix chain 'A' and resid 489 through 491 No H-bonds generated for 'chain 'A' and resid 489 through 491' Processing helix chain 'A' and resid 495 through 522 removed outlier: 4.521A pdb=" N LEU A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) 302 hydrogen bonds defined for protein. 906 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: 1.04 Time building geometry restraints manager: 1.13 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: 1121 1.34 - 1.46: 905 1.46 - 1.58: 1646 1.58 - 1.70: 0 1.70 - 1.82: 34 Bond restraints: 3706 Sorted by residual: bond pdb=" N LEU A 361 " pdb=" CA LEU A 361 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.20e-02 6.94e+03 4.32e+00 bond pdb=" CG1 ILE A 141 " pdb=" CD1 ILE A 141 " ideal model delta sigma weight residual 1.513 1.446 0.067 3.90e-02 6.57e+02 2.93e+00 bond pdb=" CG MET A 68 " pdb=" SD MET A 68 " ideal model delta sigma weight residual 1.803 1.771 0.032 2.50e-02 1.60e+03 1.61e+00 bond pdb=" CB GLU A 268 " pdb=" CG GLU A 268 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.32e+00 bond pdb=" CB PRO A 335 " pdb=" CG PRO A 335 " ideal model delta sigma weight residual 1.492 1.543 -0.051 5.00e-02 4.00e+02 1.04e+00 ... (remaining 3701 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 4849 1.72 - 3.45: 149 3.45 - 5.17: 31 5.17 - 6.89: 14 6.89 - 8.61: 10 Bond angle restraints: 5053 Sorted by residual: angle pdb=" CA MET A 68 " pdb=" CB MET A 68 " pdb=" CG MET A 68 " ideal model delta sigma weight residual 114.10 121.17 -7.07 2.00e+00 2.50e-01 1.25e+01 angle pdb=" N ILE A 141 " pdb=" CA ILE A 141 " pdb=" CB ILE A 141 " ideal model delta sigma weight residual 110.65 116.54 -5.89 1.71e+00 3.42e-01 1.19e+01 angle pdb=" N MET A 68 " pdb=" CA MET A 68 " pdb=" CB MET A 68 " ideal model delta sigma weight residual 110.16 114.90 -4.74 1.48e+00 4.57e-01 1.03e+01 angle pdb=" CA MET A 473 " pdb=" CB MET A 473 " pdb=" CG MET A 473 " ideal model delta sigma weight residual 114.10 120.43 -6.33 2.00e+00 2.50e-01 1.00e+01 angle pdb=" CA ILE A 141 " pdb=" CB ILE A 141 " pdb=" CG1 ILE A 141 " ideal model delta sigma weight residual 110.40 115.68 -5.28 1.70e+00 3.46e-01 9.66e+00 ... (remaining 5048 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 1830 15.99 - 31.98: 233 31.98 - 47.97: 75 47.97 - 63.96: 14 63.96 - 79.95: 5 Dihedral angle restraints: 2157 sinusoidal: 808 harmonic: 1349 Sorted by residual: dihedral pdb=" CB CYS A 233 " pdb=" SG CYS A 233 " pdb=" SG CYS A 236 " pdb=" CB CYS A 236 " ideal model delta sinusoidal sigma weight residual 93.00 166.71 -73.71 1 1.00e+01 1.00e-02 6.91e+01 dihedral pdb=" CB CYS A 322 " pdb=" SG CYS A 322 " pdb=" SG CYS A 354 " pdb=" CB CYS A 354 " ideal model delta sinusoidal sigma weight residual -86.00 -45.81 -40.19 1 1.00e+01 1.00e-02 2.27e+01 dihedral pdb=" CA PHE A 334 " pdb=" C PHE A 334 " pdb=" N PRO A 335 " pdb=" CA PRO A 335 " ideal model delta harmonic sigma weight residual 180.00 162.04 17.96 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 2154 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 407 0.037 - 0.075: 133 0.075 - 0.112: 48 0.112 - 0.150: 12 0.150 - 0.187: 2 Chirality restraints: 602 Sorted by residual: chirality pdb=" CB THR A 209 " pdb=" CA THR A 209 " pdb=" OG1 THR A 209 " pdb=" CG2 THR A 209 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.75e-01 chirality pdb=" CB THR A 412 " pdb=" CA THR A 412 " pdb=" OG1 THR A 412 " pdb=" CG2 THR A 412 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.00e-01 chirality pdb=" CA MET A 68 " pdb=" N MET A 68 " pdb=" C MET A 68 " pdb=" CB MET A 68 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 599 not shown) Planarity restraints: 624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 63 " -0.033 5.00e-02 4.00e+02 5.06e-02 4.09e+00 pdb=" N PRO A 64 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 64 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 64 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 296 " -0.006 2.00e-02 2.50e+03 1.42e-02 3.52e+00 pdb=" CG PHE A 296 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE A 296 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 296 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE A 296 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 296 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 296 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 230 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO A 231 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 231 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 231 " -0.022 5.00e-02 4.00e+02 ... (remaining 621 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 568 2.76 - 3.29: 3996 3.29 - 3.83: 6369 3.83 - 4.36: 6782 4.36 - 4.90: 11324 Nonbonded interactions: 29039 Sorted by model distance: nonbonded pdb=" O LEU A 58 " pdb=" OG1 THR A 62 " model vdw 2.219 3.040 nonbonded pdb=" OG1 THR A 450 " pdb=" OD1 ASN A 461 " model vdw 2.245 3.040 nonbonded pdb=" O GLY A 372 " pdb=" OG1 THR A 376 " model vdw 2.312 3.040 nonbonded pdb=" O MET A 377 " pdb=" OG1 THR A 380 " model vdw 2.322 3.040 nonbonded pdb=" OE2 GLU A 142 " pdb=" NH2 ARG A 400 " model vdw 2.334 3.120 ... (remaining 29034 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: 0.300 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 13.050 Find NCS groups from input model: 0.030 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 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 0.067 3706 Z= 0.226 Angle : 0.826 8.612 5053 Z= 0.414 Chirality : 0.044 0.187 602 Planarity : 0.005 0.051 624 Dihedral : 15.985 79.954 1287 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.62 % Allowed : 23.10 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.40), residues: 467 helix: 1.47 (0.27), residues: 372 sheet: None (None), residues: 0 loop : -1.83 (0.67), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 94 HIS 0.004 0.001 HIS A 493 PHE 0.030 0.002 PHE A 296 TYR 0.017 0.001 TYR A 362 ARG 0.005 0.000 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 PHE cc_start: 0.8201 (m-10) cc_final: 0.7573 (m-10) REVERT: A 120 ASP cc_start: 0.7306 (p0) cc_final: 0.6729 (p0) REVERT: A 138 TRP cc_start: 0.8426 (t60) cc_final: 0.7959 (t60) REVERT: A 167 ARG cc_start: 0.5113 (mtt90) cc_final: 0.4650 (tpt170) REVERT: A 268 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8208 (mp0) REVERT: A 297 ILE cc_start: 0.9518 (pt) cc_final: 0.8929 (pt) REVERT: A 319 PHE cc_start: 0.7102 (t80) cc_final: 0.6724 (t80) REVERT: A 346 TYR cc_start: 0.7927 (t80) cc_final: 0.7288 (t80) REVERT: A 384 GLN cc_start: 0.8102 (tt0) cc_final: 0.7852 (tm-30) REVERT: A 394 ARG cc_start: 0.7880 (tpt-90) cc_final: 0.7209 (tpt90) outliers start: 10 outliers final: 5 residues processed: 163 average time/residue: 0.1253 time to fit residues: 25.8091 Evaluate side-chains 142 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 137 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 487 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 0.8980 chunk 34 optimal weight: 0.0270 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 0.0010 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 overall best weight: 0.4844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.117825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.100111 restraints weight = 11192.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.102866 restraints weight = 7524.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.104823 restraints weight = 5511.205| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3706 Z= 0.206 Angle : 0.809 9.307 5053 Z= 0.413 Chirality : 0.046 0.180 602 Planarity : 0.006 0.058 624 Dihedral : 5.971 50.234 515 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.67 % Allowed : 26.51 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.40), residues: 467 helix: 1.56 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -1.52 (0.67), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 364 HIS 0.003 0.001 HIS A 493 PHE 0.031 0.002 PHE A 199 TYR 0.021 0.002 TYR A 362 ARG 0.002 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 PHE cc_start: 0.8157 (m-10) cc_final: 0.7664 (m-80) REVERT: A 70 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8923 (mp) REVERT: A 138 TRP cc_start: 0.9070 (t60) cc_final: 0.8759 (t60) REVERT: A 139 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9249 (mm) REVERT: A 142 GLU cc_start: 0.9168 (mm-30) cc_final: 0.8385 (mm-30) REVERT: A 199 PHE cc_start: 0.7686 (m-80) cc_final: 0.7432 (m-80) REVERT: A 265 LYS cc_start: 0.8320 (mttp) cc_final: 0.7998 (mptt) REVERT: A 268 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8093 (mp0) REVERT: A 297 ILE cc_start: 0.9400 (pt) cc_final: 0.9199 (pt) REVERT: A 384 GLN cc_start: 0.8392 (tt0) cc_final: 0.7857 (tm-30) REVERT: A 387 MET cc_start: 0.8767 (tpp) cc_final: 0.8367 (mpp) REVERT: A 456 MET cc_start: 0.7679 (mpp) cc_final: 0.7170 (mpp) REVERT: A 514 LEU cc_start: 0.9385 (mm) cc_final: 0.9103 (mm) outliers start: 14 outliers final: 9 residues processed: 149 average time/residue: 0.1088 time to fit residues: 21.1432 Evaluate side-chains 144 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 487 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 24 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 1 optimal weight: 3.9990 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 107 GLN ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.117298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.099495 restraints weight = 11236.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.102176 restraints weight = 7573.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.104172 restraints weight = 5575.060| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3706 Z= 0.200 Angle : 0.778 10.995 5053 Z= 0.392 Chirality : 0.046 0.161 602 Planarity : 0.006 0.060 624 Dihedral : 5.673 50.205 511 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 6.30 % Allowed : 26.25 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.40), residues: 467 helix: 1.64 (0.27), residues: 374 sheet: None (None), residues: 0 loop : -1.47 (0.66), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 94 HIS 0.003 0.001 HIS A 255 PHE 0.038 0.002 PHE A 301 TYR 0.019 0.001 TYR A 362 ARG 0.003 0.000 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 66 PHE cc_start: 0.8177 (m-10) cc_final: 0.7702 (m-80) REVERT: A 70 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8916 (mp) REVERT: A 107 GLN cc_start: 0.9376 (mt0) cc_final: 0.9096 (mm110) REVERT: A 138 TRP cc_start: 0.9048 (t60) cc_final: 0.8652 (t60) REVERT: A 139 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9181 (mm) REVERT: A 142 GLU cc_start: 0.9228 (mm-30) cc_final: 0.8073 (mm-30) REVERT: A 149 ASP cc_start: 0.9067 (m-30) cc_final: 0.8839 (m-30) REVERT: A 167 ARG cc_start: 0.4801 (mtt180) cc_final: 0.3674 (tpt170) REVERT: A 192 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6316 (mp) REVERT: A 255 HIS cc_start: 0.9364 (p90) cc_final: 0.9060 (p90) REVERT: A 268 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8111 (mp0) REVERT: A 273 ARG cc_start: 0.9044 (tpm170) cc_final: 0.8759 (tpm170) REVERT: A 384 GLN cc_start: 0.8323 (tt0) cc_final: 0.7829 (tm-30) REVERT: A 456 MET cc_start: 0.7785 (mpp) cc_final: 0.7345 (mpp) outliers start: 24 outliers final: 12 residues processed: 146 average time/residue: 0.1164 time to fit residues: 21.9879 Evaluate side-chains 139 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 487 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 19 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 4 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 25 optimal weight: 0.0000 chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.118851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.100774 restraints weight = 11335.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.103420 restraints weight = 7779.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.105097 restraints weight = 5776.306| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3706 Z= 0.208 Angle : 0.825 9.720 5053 Z= 0.408 Chirality : 0.046 0.178 602 Planarity : 0.006 0.059 624 Dihedral : 5.742 49.678 511 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.46 % Allowed : 30.18 % Favored : 65.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.40), residues: 467 helix: 1.70 (0.27), residues: 373 sheet: None (None), residues: 0 loop : -1.32 (0.64), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 94 HIS 0.002 0.001 HIS A 255 PHE 0.043 0.002 PHE A 301 TYR 0.028 0.001 TYR A 362 ARG 0.002 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 66 PHE cc_start: 0.8119 (m-10) cc_final: 0.7638 (m-80) REVERT: A 70 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8967 (mp) REVERT: A 107 GLN cc_start: 0.9251 (mt0) cc_final: 0.9048 (mm110) REVERT: A 138 TRP cc_start: 0.8986 (t60) cc_final: 0.8431 (t60) REVERT: A 142 GLU cc_start: 0.9214 (mm-30) cc_final: 0.7754 (mm-30) REVERT: A 149 ASP cc_start: 0.9122 (m-30) cc_final: 0.8894 (m-30) REVERT: A 167 ARG cc_start: 0.5123 (mtt180) cc_final: 0.3399 (tpt170) REVERT: A 192 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6298 (mp) REVERT: A 265 LYS cc_start: 0.8449 (mttp) cc_final: 0.8024 (mptt) REVERT: A 268 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8124 (mp0) REVERT: A 273 ARG cc_start: 0.9087 (tpm170) cc_final: 0.8851 (tpm170) REVERT: A 336 MET cc_start: 0.7788 (mmm) cc_final: 0.7240 (tpp) REVERT: A 384 GLN cc_start: 0.8294 (tt0) cc_final: 0.7810 (tm-30) REVERT: A 456 MET cc_start: 0.7784 (mpp) cc_final: 0.7555 (mpp) outliers start: 17 outliers final: 12 residues processed: 148 average time/residue: 0.1129 time to fit residues: 21.6957 Evaluate side-chains 142 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 487 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 35 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** 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 = 0.3872 r_free = 0.3872 target = 0.117111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.099367 restraints weight = 11445.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.102013 restraints weight = 7833.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.103949 restraints weight = 5779.533| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3706 Z= 0.223 Angle : 0.835 9.365 5053 Z= 0.411 Chirality : 0.045 0.158 602 Planarity : 0.006 0.062 624 Dihedral : 5.804 48.506 511 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 6.30 % Allowed : 30.18 % Favored : 63.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.39), residues: 467 helix: 1.62 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -1.22 (0.66), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 171 HIS 0.003 0.001 HIS A 328 PHE 0.043 0.002 PHE A 301 TYR 0.024 0.001 TYR A 362 ARG 0.002 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 PHE cc_start: 0.8144 (m-10) cc_final: 0.7657 (m-80) REVERT: A 70 ILE cc_start: 0.9238 (OUTLIER) cc_final: 0.9010 (mp) REVERT: A 106 CYS cc_start: 0.9314 (m) cc_final: 0.9067 (m) REVERT: A 138 TRP cc_start: 0.8901 (t60) cc_final: 0.8546 (t60) REVERT: A 139 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9160 (mm) REVERT: A 142 GLU cc_start: 0.9219 (mm-30) cc_final: 0.8037 (mm-30) REVERT: A 149 ASP cc_start: 0.9187 (m-30) cc_final: 0.8932 (m-30) REVERT: A 167 ARG cc_start: 0.5086 (mtt180) cc_final: 0.3662 (tpt170) REVERT: A 192 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6280 (mp) REVERT: A 255 HIS cc_start: 0.9314 (p90) cc_final: 0.9068 (p90) REVERT: A 265 LYS cc_start: 0.8474 (mttp) cc_final: 0.7966 (mptt) REVERT: A 268 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8131 (mp0) REVERT: A 273 ARG cc_start: 0.9084 (tpm170) cc_final: 0.8857 (tpm170) REVERT: A 384 GLN cc_start: 0.8300 (tt0) cc_final: 0.7847 (tm-30) REVERT: A 443 VAL cc_start: 0.9277 (OUTLIER) cc_final: 0.9013 (p) outliers start: 24 outliers final: 16 residues processed: 142 average time/residue: 0.1182 time to fit residues: 21.5874 Evaluate side-chains 148 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 487 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 42 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.118378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.099851 restraints weight = 11615.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.102299 restraints weight = 7895.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.104494 restraints weight = 5954.963| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3706 Z= 0.217 Angle : 0.861 9.400 5053 Z= 0.418 Chirality : 0.047 0.216 602 Planarity : 0.006 0.060 624 Dihedral : 5.860 50.651 511 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 6.82 % Allowed : 32.28 % Favored : 60.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.40), residues: 467 helix: 1.54 (0.27), residues: 377 sheet: None (None), residues: 0 loop : -1.35 (0.67), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 171 HIS 0.002 0.001 HIS A 328 PHE 0.043 0.002 PHE A 301 TYR 0.024 0.002 TYR A 362 ARG 0.003 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 PHE cc_start: 0.8177 (m-10) cc_final: 0.7679 (m-80) REVERT: A 70 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8976 (mp) REVERT: A 106 CYS cc_start: 0.9247 (m) cc_final: 0.8939 (m) REVERT: A 138 TRP cc_start: 0.8895 (t60) cc_final: 0.8442 (t60) REVERT: A 139 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9137 (mm) REVERT: A 142 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8156 (mm-30) REVERT: A 149 ASP cc_start: 0.9177 (m-30) cc_final: 0.8925 (m-30) REVERT: A 167 ARG cc_start: 0.4998 (mtt180) cc_final: 0.3655 (tpt170) REVERT: A 192 LEU cc_start: 0.7035 (OUTLIER) cc_final: 0.6312 (mp) REVERT: A 229 PHE cc_start: 0.6766 (t80) cc_final: 0.6287 (t80) REVERT: A 255 HIS cc_start: 0.9282 (p90) cc_final: 0.8880 (p90) REVERT: A 268 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8124 (mp0) REVERT: A 273 ARG cc_start: 0.9098 (tpm170) cc_final: 0.8870 (tpm170) REVERT: A 384 GLN cc_start: 0.8211 (tt0) cc_final: 0.7861 (tm-30) REVERT: A 443 VAL cc_start: 0.9195 (OUTLIER) cc_final: 0.8948 (p) outliers start: 26 outliers final: 16 residues processed: 146 average time/residue: 0.1100 time to fit residues: 21.0224 Evaluate side-chains 150 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 487 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 36 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** 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 = 0.3881 r_free = 0.3881 target = 0.117521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.099387 restraints weight = 11496.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.102024 restraints weight = 7832.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.104087 restraints weight = 5810.770| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3706 Z= 0.232 Angle : 0.897 9.249 5053 Z= 0.438 Chirality : 0.047 0.174 602 Planarity : 0.006 0.060 624 Dihedral : 6.001 52.656 511 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 20.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 7.87 % Allowed : 31.50 % Favored : 60.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.40), residues: 467 helix: 1.53 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -1.29 (0.69), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 94 HIS 0.003 0.001 HIS A 328 PHE 0.048 0.002 PHE A 301 TYR 0.030 0.002 TYR A 362 ARG 0.002 0.000 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 PHE cc_start: 0.8164 (m-10) cc_final: 0.7672 (m-80) REVERT: A 106 CYS cc_start: 0.9277 (m) cc_final: 0.8952 (m) REVERT: A 138 TRP cc_start: 0.8894 (t60) cc_final: 0.8587 (t60) REVERT: A 139 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9099 (mm) REVERT: A 142 GLU cc_start: 0.9245 (mm-30) cc_final: 0.8065 (mm-30) REVERT: A 149 ASP cc_start: 0.9196 (m-30) cc_final: 0.8926 (m-30) REVERT: A 167 ARG cc_start: 0.4940 (mtt180) cc_final: 0.3654 (tpt170) REVERT: A 192 LEU cc_start: 0.6908 (OUTLIER) cc_final: 0.5996 (mp) REVERT: A 229 PHE cc_start: 0.6770 (t80) cc_final: 0.6288 (t80) REVERT: A 268 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8113 (mp0) REVERT: A 273 ARG cc_start: 0.9128 (tpm170) cc_final: 0.8881 (tpm170) REVERT: A 384 GLN cc_start: 0.8161 (tt0) cc_final: 0.7803 (tm-30) REVERT: A 424 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8514 (mt) REVERT: A 443 VAL cc_start: 0.9267 (OUTLIER) cc_final: 0.9041 (p) outliers start: 30 outliers final: 20 residues processed: 145 average time/residue: 0.1161 time to fit residues: 21.8533 Evaluate side-chains 157 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 487 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 23 optimal weight: 6.9990 chunk 11 optimal weight: 0.0170 chunk 4 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.117629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.099417 restraints weight = 11367.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.102010 restraints weight = 7785.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.103923 restraints weight = 5779.489| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3706 Z= 0.234 Angle : 0.949 16.883 5053 Z= 0.456 Chirality : 0.050 0.258 602 Planarity : 0.006 0.062 624 Dihedral : 6.080 55.368 511 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 19.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 6.82 % Allowed : 34.12 % Favored : 59.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.39), residues: 467 helix: 1.41 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -1.38 (0.67), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 94 HIS 0.003 0.001 HIS A 328 PHE 0.052 0.003 PHE A 301 TYR 0.027 0.002 TYR A 362 ARG 0.002 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 PHE cc_start: 0.8224 (m-10) cc_final: 0.7958 (m-80) REVERT: A 106 CYS cc_start: 0.9258 (m) cc_final: 0.8926 (m) REVERT: A 138 TRP cc_start: 0.9032 (t60) cc_final: 0.8562 (t60) REVERT: A 139 LEU cc_start: 0.9552 (OUTLIER) cc_final: 0.9130 (mm) REVERT: A 142 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8080 (mm-30) REVERT: A 149 ASP cc_start: 0.9181 (m-30) cc_final: 0.8905 (m-30) REVERT: A 167 ARG cc_start: 0.4986 (mtt180) cc_final: 0.3762 (tpt170) REVERT: A 192 LEU cc_start: 0.6863 (OUTLIER) cc_final: 0.5910 (mp) REVERT: A 229 PHE cc_start: 0.6708 (t80) cc_final: 0.6176 (t80) REVERT: A 268 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8125 (mp0) REVERT: A 273 ARG cc_start: 0.9112 (tpm170) cc_final: 0.8849 (tpm170) REVERT: A 384 GLN cc_start: 0.8186 (tt0) cc_final: 0.7755 (tm-30) REVERT: A 443 VAL cc_start: 0.9340 (OUTLIER) cc_final: 0.9099 (p) outliers start: 26 outliers final: 21 residues processed: 144 average time/residue: 0.1188 time to fit residues: 22.3535 Evaluate side-chains 154 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 487 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 19 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 HIS ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.114499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.096745 restraints weight = 11606.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.099041 restraints weight = 7944.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.101020 restraints weight = 6041.129| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3706 Z= 0.281 Angle : 0.975 15.330 5053 Z= 0.481 Chirality : 0.051 0.294 602 Planarity : 0.006 0.063 624 Dihedral : 6.128 54.170 511 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 20.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 6.56 % Allowed : 35.17 % Favored : 58.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.39), residues: 467 helix: 1.18 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -1.31 (0.67), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 171 HIS 0.005 0.001 HIS A 328 PHE 0.053 0.003 PHE A 186 TYR 0.026 0.002 TYR A 362 ARG 0.003 0.001 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 106 CYS cc_start: 0.9225 (m) cc_final: 0.8951 (m) REVERT: A 119 LYS cc_start: 0.8096 (ptpt) cc_final: 0.7661 (ptmm) REVERT: A 138 TRP cc_start: 0.8974 (t60) cc_final: 0.8551 (t60) REVERT: A 139 LEU cc_start: 0.9577 (OUTLIER) cc_final: 0.9065 (mm) REVERT: A 142 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8011 (mm-30) REVERT: A 149 ASP cc_start: 0.9199 (m-30) cc_final: 0.8911 (m-30) REVERT: A 167 ARG cc_start: 0.4925 (mtt180) cc_final: 0.3617 (tpt170) REVERT: A 192 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6058 (mp) REVERT: A 229 PHE cc_start: 0.6673 (t80) cc_final: 0.6104 (t80) REVERT: A 268 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8154 (mp0) REVERT: A 273 ARG cc_start: 0.9100 (tpm170) cc_final: 0.8860 (tpm170) REVERT: A 384 GLN cc_start: 0.8146 (tt0) cc_final: 0.7733 (tm-30) REVERT: A 387 MET cc_start: 0.7625 (mtt) cc_final: 0.7335 (mtt) outliers start: 25 outliers final: 19 residues processed: 143 average time/residue: 0.1239 time to fit residues: 23.2908 Evaluate side-chains 152 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 487 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 30 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 17 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 18 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 HIS ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.114711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.096978 restraints weight = 11509.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.099440 restraints weight = 7841.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.101318 restraints weight = 5849.106| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3706 Z= 0.280 Angle : 1.001 14.850 5053 Z= 0.492 Chirality : 0.052 0.292 602 Planarity : 0.006 0.063 624 Dihedral : 5.863 55.282 509 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 21.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 6.04 % Allowed : 37.01 % Favored : 56.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.39), residues: 467 helix: 1.16 (0.26), residues: 370 sheet: None (None), residues: 0 loop : -1.20 (0.67), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 171 HIS 0.004 0.001 HIS A 328 PHE 0.049 0.003 PHE A 301 TYR 0.026 0.002 TYR A 362 ARG 0.003 0.000 ARG A 400 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8490 (mt) cc_final: 0.8267 (mt) REVERT: A 106 CYS cc_start: 0.9206 (m) cc_final: 0.8923 (m) REVERT: A 119 LYS cc_start: 0.8138 (ptpt) cc_final: 0.7704 (ptmm) REVERT: A 139 LEU cc_start: 0.9574 (OUTLIER) cc_final: 0.9101 (mm) REVERT: A 149 ASP cc_start: 0.9237 (m-30) cc_final: 0.8919 (m-30) REVERT: A 167 ARG cc_start: 0.4907 (mtt180) cc_final: 0.3604 (tpt170) REVERT: A 192 LEU cc_start: 0.6909 (OUTLIER) cc_final: 0.5986 (mp) REVERT: A 229 PHE cc_start: 0.6724 (t80) cc_final: 0.6165 (t80) REVERT: A 268 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8168 (mp0) REVERT: A 273 ARG cc_start: 0.9108 (tpm170) cc_final: 0.8860 (tpm170) REVERT: A 319 PHE cc_start: 0.7867 (t80) cc_final: 0.7513 (m-80) REVERT: A 329 ASP cc_start: 0.7299 (t0) cc_final: 0.4544 (t0) REVERT: A 384 GLN cc_start: 0.8198 (tt0) cc_final: 0.7796 (tm-30) REVERT: A 387 MET cc_start: 0.7640 (mtt) cc_final: 0.7392 (mtt) outliers start: 23 outliers final: 19 residues processed: 140 average time/residue: 0.1135 time to fit residues: 20.6088 Evaluate side-chains 151 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 487 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 42 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 14 optimal weight: 0.2980 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 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 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 HIS ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.116423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.098221 restraints weight = 11542.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.100825 restraints weight = 7877.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.102701 restraints weight = 5837.953| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3706 Z= 0.256 Angle : 1.017 15.129 5053 Z= 0.496 Chirality : 0.053 0.289 602 Planarity : 0.006 0.061 624 Dihedral : 5.919 57.613 509 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 21.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 5.25 % Allowed : 38.32 % Favored : 56.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.39), residues: 467 helix: 1.22 (0.26), residues: 368 sheet: None (None), residues: 0 loop : -1.18 (0.67), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 138 HIS 0.003 0.001 HIS A 328 PHE 0.053 0.003 PHE A 301 TYR 0.026 0.002 TYR A 362 ARG 0.003 0.000 ARG A 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1364.15 seconds wall clock time: 25 minutes 14.20 seconds (1514.20 seconds total)