Starting phenix.real_space_refine on Tue Feb 11 03:13:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tzs_41768/02_2025/8tzs_41768.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tzs_41768/02_2025/8tzs_41768.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tzs_41768/02_2025/8tzs_41768.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tzs_41768/02_2025/8tzs_41768.map" model { file = "/net/cci-nas-00/data/ceres_data/8tzs_41768/02_2025/8tzs_41768.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tzs_41768/02_2025/8tzs_41768.cif" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 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 36 5.16 5 C 2594 2.51 5 N 637 2.21 5 O 647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3914 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3914 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 20, 'TRANS': 459} Chain breaks: 2 Time building chain proxies: 3.21, per 1000 atoms: 0.82 Number of scatterers: 3914 At special positions: 0 Unit cell: (86.346, 103.32, 78.228, 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 36 16.00 O 647 8.00 N 637 7.00 C 2594 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 71 " distance=2.03 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 179 " distance=2.04 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: 1.17 Conformation dependent library (CDL) restraints added in 567.2 milliseconds 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 902 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 2 sheets defined 54.4% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 10 through 36 removed outlier: 3.868A pdb=" N ILE A 16 " --> pdb=" O LYS A 12 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 17 " --> pdb=" O LYS A 13 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLY A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY A 33 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 125 removed outlier: 4.043A pdb=" N GLN A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 173 Processing helix chain 'A' and resid 227 through 258 removed outlier: 3.588A pdb=" N LYS A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) Proline residue: A 243 - end of helix Processing helix chain 'A' and resid 264 through 282 removed outlier: 3.630A pdb=" N PHE A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 286 through 291 removed outlier: 4.112A pdb=" N GLY A 290 " --> pdb=" O TRP A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 322 removed outlier: 3.708A pdb=" N ASP A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 334 Processing helix chain 'A' and resid 335 through 360 Proline residue: A 341 - end of helix removed outlier: 3.753A pdb=" N VAL A 344 " --> pdb=" O GLY A 340 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N PHE A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 351 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N PHE A 352 " --> pdb=" O CYS A 348 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ASP A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 413 removed outlier: 3.611A pdb=" N SER A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS A 410 " --> pdb=" O ASN A 406 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 456 Processing helix chain 'A' and resid 473 through 493 Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 46 removed outlier: 5.976A pdb=" N ILE A 216 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA A 119 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N MET A 110 " --> pdb=" O GLU A 186 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLU A 186 " --> pdb=" O MET A 110 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N PHE A 112 " --> pdb=" O PHE A 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51 removed outlier: 6.991A pdb=" N MET A 134 " --> pdb=" O ARG A 155 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ARG A 155 " --> pdb=" O MET A 134 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL A 136 " --> pdb=" O HIS A 153 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N HIS A 153 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU A 138 " --> pdb=" O MET A 151 " (cutoff:3.500A) 219 hydrogen bonds defined for protein. 633 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: 0.98 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1185 1.35 - 1.46: 1036 1.46 - 1.58: 1747 1.58 - 1.70: 2 1.70 - 1.81: 60 Bond restraints: 4030 Sorted by residual: bond pdb=" CB PRO A 263 " pdb=" CG PRO A 263 " ideal model delta sigma weight residual 1.492 1.667 -0.175 5.00e-02 4.00e+02 1.22e+01 bond pdb=" CG PRO A 263 " pdb=" CD PRO A 263 " ideal model delta sigma weight residual 1.503 1.390 0.113 3.40e-02 8.65e+02 1.10e+01 bond pdb=" N PRO A 263 " pdb=" CD PRO A 263 " ideal model delta sigma weight residual 1.473 1.514 -0.041 1.40e-02 5.10e+03 8.64e+00 bond pdb=" N PRO A 263 " pdb=" CA PRO A 263 " ideal model delta sigma weight residual 1.465 1.444 0.020 1.11e-02 8.12e+03 3.36e+00 bond pdb=" CB PRO A 170 " pdb=" CG PRO A 170 " ideal model delta sigma weight residual 1.492 1.580 -0.088 5.00e-02 4.00e+02 3.08e+00 ... (remaining 4025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 5404 3.21 - 6.41: 40 6.41 - 9.62: 7 9.62 - 12.82: 4 12.82 - 16.03: 2 Bond angle restraints: 5457 Sorted by residual: angle pdb=" CA PRO A 263 " pdb=" N PRO A 263 " pdb=" CD PRO A 263 " ideal model delta sigma weight residual 112.00 95.97 16.03 1.40e+00 5.10e-01 1.31e+02 angle pdb=" N PRO A 263 " pdb=" CD PRO A 263 " pdb=" CG PRO A 263 " ideal model delta sigma weight residual 103.20 93.36 9.84 1.50e+00 4.44e-01 4.30e+01 angle pdb=" CA PRO A 170 " pdb=" N PRO A 170 " pdb=" CD PRO A 170 " ideal model delta sigma weight residual 112.00 105.41 6.59 1.40e+00 5.10e-01 2.22e+01 angle pdb=" CA LEU A 440 " pdb=" CB LEU A 440 " pdb=" CG LEU A 440 " ideal model delta sigma weight residual 116.30 131.82 -15.52 3.50e+00 8.16e-02 1.97e+01 angle pdb=" CA CYS A 179 " pdb=" CB CYS A 179 " pdb=" SG CYS A 179 " ideal model delta sigma weight residual 114.40 124.10 -9.70 2.30e+00 1.89e-01 1.78e+01 ... (remaining 5452 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 2018 16.01 - 32.02: 233 32.02 - 48.04: 78 48.04 - 64.05: 10 64.05 - 80.06: 5 Dihedral angle restraints: 2344 sinusoidal: 951 harmonic: 1393 Sorted by residual: dihedral pdb=" CA CYS A 179 " pdb=" C CYS A 179 " pdb=" N ASP A 180 " pdb=" CA ASP A 180 " ideal model delta harmonic sigma weight residual -180.00 -131.97 -48.03 0 5.00e+00 4.00e-02 9.23e+01 dihedral pdb=" CA LYS A 161 " pdb=" C LYS A 161 " pdb=" N CYS A 162 " pdb=" CA CYS A 162 " ideal model delta harmonic sigma weight residual 180.00 -148.29 -31.71 0 5.00e+00 4.00e-02 4.02e+01 dihedral pdb=" CA GLU A 178 " pdb=" C GLU A 178 " pdb=" N CYS A 179 " pdb=" CA CYS A 179 " ideal model delta harmonic sigma weight residual 180.00 -157.47 -22.53 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 2341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 457 0.053 - 0.106: 128 0.106 - 0.158: 8 0.158 - 0.211: 1 0.211 - 0.264: 3 Chirality restraints: 597 Sorted by residual: chirality pdb=" CB ILE A 216 " pdb=" CA ILE A 216 " pdb=" CG1 ILE A 216 " pdb=" CG2 ILE A 216 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA CYS A 179 " pdb=" N CYS A 179 " pdb=" C CYS A 179 " pdb=" CB CYS A 179 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA PRO A 263 " pdb=" N PRO A 263 " pdb=" C PRO A 263 " pdb=" CB PRO A 263 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 594 not shown) Planarity restraints: 672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 169 " 0.070 5.00e-02 4.00e+02 1.03e-01 1.68e+01 pdb=" N PRO A 170 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO A 170 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 170 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 262 " -0.068 5.00e-02 4.00e+02 9.20e-02 1.35e+01 pdb=" N PRO A 263 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO A 263 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 263 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 490 " 0.010 2.00e-02 2.50e+03 1.10e-02 2.12e+00 pdb=" CG PHE A 490 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE A 490 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 490 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 490 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 490 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 490 " 0.001 2.00e-02 2.50e+03 ... (remaining 669 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 155 2.72 - 3.26: 4179 3.26 - 3.81: 6425 3.81 - 4.35: 7251 4.35 - 4.90: 12405 Nonbonded interactions: 30415 Sorted by model distance: nonbonded pdb=" OD1 ASN A 8 " pdb=" OG SER A 495 " model vdw 2.170 3.040 nonbonded pdb=" NH1 ARG A 158 " pdb=" O PRO A 183 " model vdw 2.171 3.120 nonbonded pdb=" O MET A 9 " pdb=" NH2 ARG A 431 " model vdw 2.174 3.120 nonbonded pdb=" O THR A 371 " pdb=" N GLY A 374 " model vdw 2.234 3.120 nonbonded pdb=" O GLN A 326 " pdb=" NH1 ARG A 329 " model vdw 2.289 3.120 ... (remaining 30410 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 13.970 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 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 : 0.005 0.175 4030 Z= 0.323 Angle : 0.871 16.031 5457 Z= 0.477 Chirality : 0.047 0.264 597 Planarity : 0.007 0.103 672 Dihedral : 15.830 80.062 1436 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.24 % Allowed : 20.57 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % 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: 0.65 (0.38), residues: 474 helix: 1.37 (0.32), residues: 223 sheet: 0.18 (0.61), residues: 67 loop : -0.56 (0.48), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 66 HIS 0.004 0.001 HIS A 192 PHE 0.026 0.002 PHE A 490 TYR 0.016 0.002 TYR A 45 ARG 0.002 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7109 (mm-30) outliers start: 1 outliers final: 0 residues processed: 98 average time/residue: 0.1383 time to fit residues: 17.5981 Evaluate side-chains 92 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.0770 chunk 36 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.156791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.126741 restraints weight = 8311.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.130303 restraints weight = 4787.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.132789 restraints weight = 3362.866| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 4030 Z= 0.211 Angle : 0.649 10.594 5457 Z= 0.337 Chirality : 0.045 0.256 597 Planarity : 0.005 0.060 672 Dihedral : 5.384 40.040 511 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.55 % Allowed : 17.97 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: 0.96 (0.38), residues: 474 helix: 1.55 (0.32), residues: 229 sheet: 0.46 (0.61), residues: 67 loop : -0.44 (0.50), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.004 0.001 HIS A 192 PHE 0.016 0.002 PHE A 318 TYR 0.012 0.002 TYR A 45 ARG 0.002 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 478 TYR cc_start: 0.8009 (t80) cc_final: 0.7679 (t80) outliers start: 15 outliers final: 12 residues processed: 111 average time/residue: 0.1292 time to fit residues: 18.5608 Evaluate side-chains 107 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 439 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 16 optimal weight: 0.1980 chunk 47 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 45 optimal weight: 0.0050 chunk 27 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 25 optimal weight: 0.0030 overall best weight: 0.4204 ------------------------------------------------------------------------------- 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 = 0.4057 r_free = 0.4057 target = 0.158935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.130182 restraints weight = 8368.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.133459 restraints weight = 5047.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.135801 restraints weight = 3615.405| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4030 Z= 0.169 Angle : 0.608 12.451 5457 Z= 0.309 Chirality : 0.043 0.202 597 Planarity : 0.004 0.047 672 Dihedral : 4.966 36.356 511 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.78 % Allowed : 19.15 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: 1.28 (0.39), residues: 474 helix: 1.85 (0.33), residues: 229 sheet: 0.63 (0.58), residues: 67 loop : -0.33 (0.51), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.003 0.001 HIS A 192 PHE 0.016 0.001 PHE A 490 TYR 0.015 0.001 TYR A 45 ARG 0.002 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 489 MET cc_start: 0.8715 (mtm) cc_final: 0.8455 (mtm) outliers start: 16 outliers final: 13 residues processed: 113 average time/residue: 0.1362 time to fit residues: 19.8945 Evaluate side-chains 108 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 13 optimal weight: 10.0000 chunk 33 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 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 198 ASN A 331 HIS ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.156763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.128164 restraints weight = 8261.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.131542 restraints weight = 4926.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.133903 restraints weight = 3503.369| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4030 Z= 0.201 Angle : 0.614 12.233 5457 Z= 0.309 Chirality : 0.042 0.149 597 Planarity : 0.004 0.038 672 Dihedral : 4.847 32.354 511 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.96 % Allowed : 19.86 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: 1.50 (0.39), residues: 474 helix: 2.08 (0.33), residues: 227 sheet: 0.62 (0.57), residues: 74 loop : -0.25 (0.51), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 66 HIS 0.003 0.001 HIS A 496 PHE 0.017 0.002 PHE A 490 TYR 0.027 0.002 TYR A 140 ARG 0.002 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 17 residues processed: 109 average time/residue: 0.1288 time to fit residues: 18.1168 Evaluate side-chains 109 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 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 = 0.4025 r_free = 0.4025 target = 0.156061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.127360 restraints weight = 8567.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.130744 restraints weight = 5116.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.133101 restraints weight = 3624.283| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4030 Z= 0.202 Angle : 0.618 13.754 5457 Z= 0.309 Chirality : 0.042 0.141 597 Planarity : 0.004 0.035 672 Dihedral : 4.743 29.581 511 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 5.67 % Allowed : 20.33 % Favored : 74.00 % 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: 1.56 (0.39), residues: 474 helix: 2.07 (0.33), residues: 228 sheet: 0.83 (0.58), residues: 74 loop : -0.24 (0.51), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 66 HIS 0.003 0.001 HIS A 192 PHE 0.018 0.002 PHE A 490 TYR 0.015 0.001 TYR A 45 ARG 0.002 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 432 PHE cc_start: 0.6855 (OUTLIER) cc_final: 0.5941 (t80) outliers start: 24 outliers final: 20 residues processed: 113 average time/residue: 0.1321 time to fit residues: 19.3713 Evaluate side-chains 117 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 2 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 36 optimal weight: 0.0050 chunk 26 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 17 optimal weight: 0.0970 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 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 = 0.4053 r_free = 0.4053 target = 0.158334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.129692 restraints weight = 8395.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.133121 restraints weight = 5004.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.135494 restraints weight = 3566.450| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4030 Z= 0.168 Angle : 0.611 13.595 5457 Z= 0.303 Chirality : 0.041 0.138 597 Planarity : 0.004 0.042 672 Dihedral : 4.592 26.445 511 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 5.20 % Allowed : 21.75 % Favored : 73.05 % 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: 1.67 (0.39), residues: 474 helix: 2.10 (0.33), residues: 230 sheet: 0.88 (0.58), residues: 73 loop : -0.11 (0.51), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 148 HIS 0.003 0.001 HIS A 192 PHE 0.016 0.001 PHE A 490 TYR 0.011 0.001 TYR A 45 ARG 0.002 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 101 MET cc_start: 0.8079 (ptp) cc_final: 0.7632 (pmm) REVERT: A 145 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.7745 (p90) REVERT: A 281 ASN cc_start: 0.8613 (m-40) cc_final: 0.8383 (t0) REVERT: A 432 PHE cc_start: 0.6771 (OUTLIER) cc_final: 0.5858 (t80) outliers start: 22 outliers final: 16 residues processed: 117 average time/residue: 0.1405 time to fit residues: 20.9361 Evaluate side-chains 119 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 7 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 9 optimal weight: 0.0980 chunk 26 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 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 = 0.4056 r_free = 0.4056 target = 0.158703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.130533 restraints weight = 8114.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.133955 restraints weight = 4806.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.136418 restraints weight = 3364.734| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4030 Z= 0.184 Angle : 0.644 14.446 5457 Z= 0.314 Chirality : 0.042 0.137 597 Planarity : 0.004 0.040 672 Dihedral : 4.581 25.105 511 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 5.20 % Allowed : 21.75 % Favored : 73.05 % 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: 1.70 (0.39), residues: 474 helix: 2.10 (0.33), residues: 230 sheet: 0.94 (0.57), residues: 75 loop : -0.08 (0.51), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 66 HIS 0.003 0.001 HIS A 496 PHE 0.016 0.002 PHE A 490 TYR 0.018 0.002 TYR A 140 ARG 0.002 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 219 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8471 (pt) REVERT: A 281 ASN cc_start: 0.8661 (OUTLIER) cc_final: 0.8411 (t0) REVERT: A 432 PHE cc_start: 0.6770 (OUTLIER) cc_final: 0.5865 (t80) outliers start: 22 outliers final: 17 residues processed: 120 average time/residue: 0.1333 time to fit residues: 20.7443 Evaluate side-chains 123 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 1.9990 chunk 14 optimal weight: 0.0870 chunk 25 optimal weight: 0.7980 chunk 9 optimal weight: 0.0970 chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.5956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 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 = 0.4060 r_free = 0.4060 target = 0.159016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.130511 restraints weight = 8144.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.133779 restraints weight = 4926.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.136141 restraints weight = 3502.070| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4030 Z= 0.181 Angle : 0.644 13.562 5457 Z= 0.320 Chirality : 0.043 0.137 597 Planarity : 0.004 0.037 672 Dihedral : 4.709 24.106 511 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.96 % Allowed : 23.17 % Favored : 71.87 % 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: 1.72 (0.39), residues: 474 helix: 2.11 (0.33), residues: 230 sheet: 1.49 (0.64), residues: 61 loop : -0.21 (0.48), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 148 HIS 0.003 0.000 HIS A 496 PHE 0.018 0.001 PHE A 490 TYR 0.021 0.002 TYR A 392 ARG 0.003 0.000 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: A 101 MET cc_start: 0.8051 (ptp) cc_final: 0.7682 (pmm) REVERT: A 145 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.7811 (p90) REVERT: A 281 ASN cc_start: 0.8599 (m-40) cc_final: 0.8385 (t0) REVERT: A 432 PHE cc_start: 0.6742 (OUTLIER) cc_final: 0.5826 (t80) REVERT: A 478 TYR cc_start: 0.8181 (t80) cc_final: 0.7975 (t80) outliers start: 21 outliers final: 17 residues processed: 120 average time/residue: 0.1252 time to fit residues: 19.4782 Evaluate side-chains 121 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 0.0040 chunk 40 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 18 optimal weight: 0.2980 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 23 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.158673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.130125 restraints weight = 8276.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.133440 restraints weight = 4923.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.135758 restraints weight = 3485.169| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4030 Z= 0.182 Angle : 0.656 15.570 5457 Z= 0.321 Chirality : 0.043 0.145 597 Planarity : 0.004 0.039 672 Dihedral : 4.664 23.917 511 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.73 % Allowed : 23.40 % Favored : 71.87 % 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: 1.76 (0.39), residues: 474 helix: 2.14 (0.33), residues: 230 sheet: 1.44 (0.63), residues: 61 loop : -0.17 (0.48), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 66 HIS 0.001 0.000 HIS A 100 PHE 0.020 0.001 PHE A 398 TYR 0.018 0.002 TYR A 392 ARG 0.003 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.8086 (ptp) cc_final: 0.7689 (pmm) REVERT: A 145 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.7796 (p90) REVERT: A 281 ASN cc_start: 0.8668 (OUTLIER) cc_final: 0.8374 (t0) REVERT: A 432 PHE cc_start: 0.6774 (OUTLIER) cc_final: 0.5849 (t80) outliers start: 20 outliers final: 15 residues processed: 118 average time/residue: 0.1437 time to fit residues: 21.4340 Evaluate side-chains 120 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 46 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 21 optimal weight: 10.0000 chunk 38 optimal weight: 0.0870 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 3 optimal weight: 0.7980 chunk 9 optimal weight: 0.0670 overall best weight: 0.4096 ------------------------------------------------------------------------------- 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 = 0.4069 r_free = 0.4069 target = 0.160052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.131624 restraints weight = 8247.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.135016 restraints weight = 4893.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.137384 restraints weight = 3444.638| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4030 Z= 0.179 Angle : 0.677 15.826 5457 Z= 0.336 Chirality : 0.043 0.146 597 Planarity : 0.004 0.039 672 Dihedral : 4.560 22.858 511 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.55 % Allowed : 24.35 % Favored : 72.10 % 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: 1.66 (0.39), residues: 474 helix: 2.01 (0.33), residues: 232 sheet: 1.53 (0.63), residues: 61 loop : -0.21 (0.49), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 148 HIS 0.002 0.000 HIS A 153 PHE 0.039 0.002 PHE A 398 TYR 0.018 0.002 TYR A 392 ARG 0.003 0.000 ARG A 158 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 101 MET cc_start: 0.8011 (ptp) cc_final: 0.7628 (pmm) REVERT: A 281 ASN cc_start: 0.8567 (m-40) cc_final: 0.8360 (t0) REVERT: A 432 PHE cc_start: 0.6789 (OUTLIER) cc_final: 0.5869 (t80) outliers start: 15 outliers final: 12 residues processed: 112 average time/residue: 0.1355 time to fit residues: 19.5028 Evaluate side-chains 114 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 1 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.0670 chunk 21 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 9 optimal weight: 0.0770 chunk 43 optimal weight: 0.9980 overall best weight: 0.4676 ------------------------------------------------------------------------------- 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 = 0.4071 r_free = 0.4071 target = 0.160444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.132133 restraints weight = 8110.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.135459 restraints weight = 4845.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.137834 restraints weight = 3431.693| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4030 Z= 0.187 Angle : 0.683 15.971 5457 Z= 0.336 Chirality : 0.043 0.149 597 Planarity : 0.004 0.037 672 Dihedral : 4.535 22.427 511 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.02 % Allowed : 24.35 % Favored : 71.63 % 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: 1.55 (0.39), residues: 474 helix: 1.92 (0.33), residues: 230 sheet: 1.52 (0.61), residues: 61 loop : -0.26 (0.48), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 66 HIS 0.002 0.000 HIS A 153 PHE 0.035 0.002 PHE A 398 TYR 0.017 0.002 TYR A 392 ARG 0.003 0.000 ARG A 303 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1670.03 seconds wall clock time: 30 minutes 36.39 seconds (1836.39 seconds total)