Starting phenix.real_space_refine on Tue Mar 11 18:41:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rl8_19334/03_2025/8rl8_19334_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rl8_19334/03_2025/8rl8_19334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rl8_19334/03_2025/8rl8_19334.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rl8_19334/03_2025/8rl8_19334.map" model { file = "/net/cci-nas-00/data/ceres_data/8rl8_19334/03_2025/8rl8_19334_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rl8_19334/03_2025/8rl8_19334_trim.cif" } resolution = 2.79 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= 0.011 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: 5 Type Number sf(0) Gaussians S 17 5.16 5 C 2116 2.51 5 N 526 2.21 5 O 558 1.98 5 H 3252 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6469 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 6445 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 12, 'TRANS': 408} Chain breaks: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 4.40, per 1000 atoms: 0.68 Number of scatterers: 6469 At special positions: 0 Unit cell: (82.071, 72.952, 67.978, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 17 16.00 O 558 8.00 N 526 7.00 C 2116 6.00 H 3252 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 828.1 milliseconds 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 764 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 0 sheets defined 94.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 100 through 125 removed outlier: 4.716A pdb=" N VAL A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ALA A 123 " --> pdb=" O ARG A 119 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY A 124 " --> pdb=" O TYR A 120 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 125 " --> pdb=" O THR A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 136 through 165 removed outlier: 3.686A pdb=" N LEU A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLN A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) Proline residue: A 156 - end of helix Processing helix chain 'A' and resid 166 through 186 removed outlier: 3.718A pdb=" N ILE A 170 " --> pdb=" O ASN A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 221 removed outlier: 3.691A pdb=" N VAL A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Proline residue: A 215 - end of helix Processing helix chain 'A' and resid 226 through 257 removed outlier: 4.321A pdb=" N ILE A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Proline residue: A 239 - end of helix Processing helix chain 'A' and resid 258 through 263 Processing helix chain 'A' and resid 264 through 280 removed outlier: 4.207A pdb=" N VAL A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 269 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 279 " --> pdb=" O THR A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 310 Processing helix chain 'A' and resid 312 through 347 Proline residue: A 337 - end of helix Processing helix chain 'A' and resid 360 through 392 removed outlier: 3.654A pdb=" N PHE A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS A 391 " --> pdb=" O TRP A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 421 removed outlier: 3.859A pdb=" N LEU A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE A 415 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 416 " --> pdb=" O CYS A 412 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LYS A 419 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER A 420 " --> pdb=" O VAL A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 451 removed outlier: 3.731A pdb=" N ALA A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN A 439 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N TRP A 440 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA A 441 " --> pdb=" O PHE A 437 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ALA A 444 " --> pdb=" O TRP A 440 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 455 through 471 Processing helix chain 'A' and resid 474 through 490 Processing helix chain 'A' and resid 493 through 506 Processing helix chain 'A' and resid 506 through 525 removed outlier: 4.132A pdb=" N PHE A 510 " --> pdb=" O MET A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 539 283 hydrogen bonds defined for protein. 840 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: 2.51 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3244 1.03 - 1.23: 8 1.23 - 1.42: 1389 1.42 - 1.61: 1876 1.61 - 1.81: 26 Bond restraints: 6543 Sorted by residual: bond pdb=" C3' LMT A 601 " pdb=" O3' LMT A 601 " ideal model delta sigma weight residual 1.404 1.363 0.041 2.00e-02 2.50e+03 4.25e+00 bond pdb=" C7 LMT A 601 " pdb=" C8 LMT A 601 " ideal model delta sigma weight residual 1.529 1.491 0.038 2.00e-02 2.50e+03 3.64e+00 bond pdb=" C6' LMT A 601 " pdb=" O6' LMT A 601 " ideal model delta sigma weight residual 1.407 1.369 0.038 2.00e-02 2.50e+03 3.60e+00 bond pdb=" C4 LMT A 601 " pdb=" C5 LMT A 601 " ideal model delta sigma weight residual 1.526 1.490 0.036 2.00e-02 2.50e+03 3.33e+00 bond pdb=" C8 LMT A 601 " pdb=" C9 LMT A 601 " ideal model delta sigma weight residual 1.531 1.495 0.036 2.00e-02 2.50e+03 3.18e+00 ... (remaining 6538 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 11670 1.81 - 3.62: 99 3.62 - 5.43: 14 5.43 - 7.25: 2 7.25 - 9.06: 3 Bond angle restraints: 11788 Sorted by residual: angle pdb=" N TRP A 178 " pdb=" CA TRP A 178 " pdb=" CB TRP A 178 " ideal model delta sigma weight residual 110.30 115.08 -4.78 1.54e+00 4.22e-01 9.65e+00 angle pdb=" C2 LMT A 601 " pdb=" C3 LMT A 601 " pdb=" C4 LMT A 601 " ideal model delta sigma weight residual 117.09 108.03 9.06 3.00e+00 1.11e-01 9.12e+00 angle pdb=" C PHE A 177 " pdb=" N TRP A 178 " pdb=" CA TRP A 178 " ideal model delta sigma weight residual 120.68 115.63 5.05 1.70e+00 3.46e-01 8.84e+00 angle pdb=" CA TRP A 178 " pdb=" CB TRP A 178 " pdb=" CG TRP A 178 " ideal model delta sigma weight residual 113.60 119.06 -5.46 1.90e+00 2.77e-01 8.26e+00 angle pdb=" C10 LMT A 601 " pdb=" C9 LMT A 601 " pdb=" C8 LMT A 601 " ideal model delta sigma weight residual 116.03 107.82 8.21 3.00e+00 1.11e-01 7.50e+00 ... (remaining 11783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.41: 2772 16.41 - 32.82: 220 32.82 - 49.22: 46 49.22 - 65.63: 61 65.63 - 82.04: 2 Dihedral angle restraints: 3101 sinusoidal: 1638 harmonic: 1463 Sorted by residual: dihedral pdb=" CA ARG A 342 " pdb=" CB ARG A 342 " pdb=" CG ARG A 342 " pdb=" CD ARG A 342 " ideal model delta sinusoidal sigma weight residual -60.00 -103.91 43.91 3 1.50e+01 4.44e-03 7.90e+00 dihedral pdb=" CB MET A 230 " pdb=" CG MET A 230 " pdb=" SD MET A 230 " pdb=" CE MET A 230 " ideal model delta sinusoidal sigma weight residual 60.00 102.50 -42.50 3 1.50e+01 4.44e-03 7.63e+00 dihedral pdb=" CA LYS A 391 " pdb=" CB LYS A 391 " pdb=" CG LYS A 391 " pdb=" CD LYS A 391 " ideal model delta sinusoidal sigma weight residual -180.00 -138.28 -41.72 3 1.50e+01 4.44e-03 7.47e+00 ... (remaining 3098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 418 0.039 - 0.079: 87 0.079 - 0.118: 22 0.118 - 0.158: 2 0.158 - 0.197: 2 Chirality restraints: 531 Sorted by residual: chirality pdb=" C4' LMT A 601 " pdb=" C3' LMT A 601 " pdb=" C5' LMT A 601 " pdb=" O1B LMT A 601 " both_signs ideal model delta sigma weight residual False -2.55 -2.75 0.20 2.00e-01 2.50e+01 9.70e-01 chirality pdb=" C5' LMT A 601 " pdb=" C4' LMT A 601 " pdb=" C6' LMT A 601 " pdb=" O5' LMT A 601 " both_signs ideal model delta sigma weight residual False -2.51 -2.32 -0.19 2.00e-01 2.50e+01 8.94e-01 chirality pdb=" CA ILE A 175 " pdb=" N ILE A 175 " pdb=" C ILE A 175 " pdb=" CB ILE A 175 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.50e-01 ... (remaining 528 not shown) Planarity restraints: 949 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 178 " -0.019 2.00e-02 2.50e+03 1.25e-02 6.25e+00 pdb=" CG TRP A 178 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP A 178 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP A 178 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 178 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 178 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 178 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 178 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 178 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 178 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP A 178 " -0.007 2.00e-02 2.50e+03 pdb=" HE1 TRP A 178 " -0.003 2.00e-02 2.50e+03 pdb=" HE3 TRP A 178 " 0.002 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 178 " 0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 178 " -0.000 2.00e-02 2.50e+03 pdb=" HH2 TRP A 178 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 508 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO A 509 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 509 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 509 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 188 " 0.029 5.00e-02 4.00e+02 4.44e-02 3.16e+00 pdb=" N PRO A 189 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 189 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 189 " 0.025 5.00e-02 4.00e+02 ... (remaining 946 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 660 2.24 - 2.83: 14649 2.83 - 3.42: 18019 3.42 - 4.01: 23277 4.01 - 4.60: 36325 Nonbonded interactions: 92930 Sorted by model distance: nonbonded pdb=" O PHE A 183 " pdb=" HG SER A 186 " model vdw 1.652 2.450 nonbonded pdb=" HH TYR A 315 " pdb=" O ALA A 459 " model vdw 1.711 2.450 nonbonded pdb=" O SER A 483 " pdb=" HG SER A 500 " model vdw 1.712 2.450 nonbonded pdb=" HG SER A 150 " pdb=" O GLY A 201 " model vdw 1.768 2.450 nonbonded pdb="HE22 GLN A 344 " pdb=" OD1 ASP A 362 " model vdw 1.829 2.450 ... (remaining 92925 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.980 Find NCS groups from input model: 0.040 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:19.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 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 : 0.003 0.041 3291 Z= 0.219 Angle : 0.590 9.058 4471 Z= 0.305 Chirality : 0.037 0.197 531 Planarity : 0.004 0.046 544 Dihedral : 12.359 82.040 1143 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.43 (0.41), residues: 415 helix: 1.31 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -1.13 (0.80), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 178 HIS 0.003 0.001 HIS A 341 PHE 0.017 0.001 PHE A 526 TYR 0.014 0.001 TYR A 449 ARG 0.004 0.001 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 PHE cc_start: 0.8404 (t80) cc_final: 0.8001 (t80) REVERT: A 227 ARG cc_start: 0.7239 (ttp-170) cc_final: 0.6942 (ttm-80) REVERT: A 366 PHE cc_start: 0.7826 (t80) cc_final: 0.7436 (t80) outliers start: 0 outliers final: 1 residues processed: 74 average time/residue: 1.7668 time to fit residues: 136.2727 Evaluate side-chains 70 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 0.0970 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 393 GLN A 536 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.156611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.145194 restraints weight = 12954.782| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 1.68 r_work: 0.3906 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3789 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 3291 Z= 0.442 Angle : 0.671 7.859 4471 Z= 0.363 Chirality : 0.042 0.150 531 Planarity : 0.006 0.055 544 Dihedral : 5.141 40.995 488 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.41 % Allowed : 11.14 % Favored : 86.45 % 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: 1.35 (0.40), residues: 415 helix: 1.21 (0.26), residues: 364 sheet: None (None), residues: 0 loop : -0.98 (0.84), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP A 178 HIS 0.007 0.002 HIS A 341 PHE 0.022 0.003 PHE A 526 TYR 0.012 0.002 TYR A 503 ARG 0.003 0.001 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Evaluate side-chains 79 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 ARG cc_start: 0.7480 (ttp-170) cc_final: 0.7188 (ttm-80) REVERT: A 389 ARG cc_start: 0.6620 (OUTLIER) cc_final: 0.3606 (mtp180) REVERT: A 390 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.7032 (tt) outliers start: 8 outliers final: 5 residues processed: 73 average time/residue: 1.8602 time to fit residues: 141.0383 Evaluate side-chains 77 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 311 ARG Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 448 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 0.3980 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 33 optimal weight: 0.3980 chunk 28 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 0.1980 chunk 4 optimal weight: 0.0980 chunk 8 optimal weight: 0.0870 chunk 7 optimal weight: 0.0770 chunk 22 optimal weight: 0.5980 overall best weight: 0.1716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.161281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.149908 restraints weight = 13094.482| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 1.66 r_work: 0.3959 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3844 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3291 Z= 0.184 Angle : 0.516 5.280 4471 Z= 0.272 Chirality : 0.036 0.130 531 Planarity : 0.004 0.052 544 Dihedral : 3.762 20.343 485 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.71 % Allowed : 11.75 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.41), residues: 415 helix: 1.83 (0.27), residues: 363 sheet: None (None), residues: 0 loop : -0.74 (0.85), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 178 HIS 0.004 0.001 HIS A 341 PHE 0.013 0.001 PHE A 410 TYR 0.009 0.001 TYR A 339 ARG 0.001 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Evaluate side-chains 78 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 ARG cc_start: 0.7493 (ttp-170) cc_final: 0.7273 (ttm-80) REVERT: A 242 SER cc_start: 0.8255 (p) cc_final: 0.8013 (m) REVERT: A 390 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.7013 (tt) outliers start: 9 outliers final: 4 residues processed: 71 average time/residue: 2.4420 time to fit residues: 182.5012 Evaluate side-chains 72 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 427 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 0.0670 chunk 1 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 0.0980 chunk 8 optimal weight: 0.2980 chunk 15 optimal weight: 0.9980 chunk 5 optimal weight: 0.3980 overall best weight: 0.2518 ------------------------------------------------------------------------------- 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 = 0.4153 r_free = 0.4153 target = 0.160562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.148870 restraints weight = 13224.519| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 1.72 r_work: 0.3945 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3828 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3291 Z= 0.208 Angle : 0.519 6.221 4471 Z= 0.274 Chirality : 0.036 0.128 531 Planarity : 0.004 0.051 544 Dihedral : 3.692 22.064 485 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.41 % Allowed : 16.27 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.41), residues: 415 helix: 1.91 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.10 (0.84), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 178 HIS 0.004 0.001 HIS A 341 PHE 0.014 0.001 PHE A 410 TYR 0.008 0.001 TYR A 339 ARG 0.001 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Evaluate side-chains 75 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 ARG cc_start: 0.7515 (ttp-170) cc_final: 0.7283 (ttm-80) REVERT: A 242 SER cc_start: 0.8312 (p) cc_final: 0.8075 (m) REVERT: A 261 TRP cc_start: 0.7429 (m100) cc_final: 0.6407 (m100) REVERT: A 390 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.7069 (tt) outliers start: 8 outliers final: 6 residues processed: 70 average time/residue: 1.8816 time to fit residues: 136.7277 Evaluate side-chains 75 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 427 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 28 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 39 optimal weight: 0.2980 chunk 34 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 1 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.4115 r_free = 0.4115 target = 0.157115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.145375 restraints weight = 13058.274| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 1.74 r_work: 0.3905 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3784 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3291 Z= 0.336 Angle : 0.566 5.623 4471 Z= 0.308 Chirality : 0.038 0.140 531 Planarity : 0.005 0.051 544 Dihedral : 4.028 31.006 485 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.71 % Allowed : 17.77 % Favored : 79.52 % 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: 2.03 (0.41), residues: 415 helix: 1.65 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -1.00 (0.92), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 178 HIS 0.006 0.001 HIS A 341 PHE 0.018 0.002 PHE A 410 TYR 0.010 0.002 TYR A 339 ARG 0.002 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Evaluate side-chains 84 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 ARG cc_start: 0.7594 (ttp-170) cc_final: 0.7332 (ttm-80) REVERT: A 242 SER cc_start: 0.8334 (p) cc_final: 0.8132 (m) REVERT: A 390 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7073 (tt) outliers start: 9 outliers final: 7 residues processed: 78 average time/residue: 1.8583 time to fit residues: 150.4933 Evaluate side-chains 81 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 445 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 37 optimal weight: 0.0870 chunk 29 optimal weight: 0.4980 chunk 21 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.156014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.144403 restraints weight = 13125.617| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 1.72 r_work: 0.3885 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3764 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3291 Z= 0.315 Angle : 0.558 5.593 4471 Z= 0.301 Chirality : 0.038 0.138 531 Planarity : 0.005 0.050 544 Dihedral : 4.090 32.236 485 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.92 % Allowed : 18.37 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.41), residues: 415 helix: 1.62 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -0.87 (0.93), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 178 HIS 0.005 0.001 HIS A 341 PHE 0.019 0.002 PHE A 410 TYR 0.010 0.002 TYR A 339 ARG 0.002 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Evaluate side-chains 86 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 ARG cc_start: 0.7596 (ttp-170) cc_final: 0.7377 (ttm-80) REVERT: A 242 SER cc_start: 0.8289 (p) cc_final: 0.8080 (m) REVERT: A 390 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7095 (tt) outliers start: 13 outliers final: 6 residues processed: 77 average time/residue: 1.8817 time to fit residues: 150.5027 Evaluate side-chains 80 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 445 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 0.4980 chunk 22 optimal weight: 0.0870 chunk 29 optimal weight: 0.4980 chunk 19 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 chunk 27 optimal weight: 0.4980 chunk 38 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 overall best weight: 0.3958 ------------------------------------------------------------------------------- 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 = 0.4111 r_free = 0.4111 target = 0.157407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.145767 restraints weight = 13386.802| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 1.76 r_work: 0.3890 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3767 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3291 Z= 0.275 Angle : 0.541 5.508 4471 Z= 0.291 Chirality : 0.037 0.136 531 Planarity : 0.005 0.050 544 Dihedral : 4.052 31.579 485 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.61 % Allowed : 18.98 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.41), residues: 415 helix: 1.76 (0.27), residues: 367 sheet: None (None), residues: 0 loop : -0.90 (0.94), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 178 HIS 0.005 0.001 HIS A 341 PHE 0.017 0.002 PHE A 410 TYR 0.011 0.001 TYR A 339 ARG 0.002 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Evaluate side-chains 86 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 ARG cc_start: 0.7610 (ttp-170) cc_final: 0.7384 (ttm-80) REVERT: A 242 SER cc_start: 0.8297 (p) cc_final: 0.8084 (m) REVERT: A 390 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.7097 (tt) outliers start: 12 outliers final: 8 residues processed: 78 average time/residue: 1.7966 time to fit residues: 145.7427 Evaluate side-chains 82 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 536 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 0.0980 chunk 20 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 13 optimal weight: 0.1980 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.4107 r_free = 0.4107 target = 0.156977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.145210 restraints weight = 13288.273| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 1.73 r_work: 0.3903 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3783 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3291 Z= 0.301 Angle : 0.551 5.511 4471 Z= 0.298 Chirality : 0.038 0.138 531 Planarity : 0.005 0.050 544 Dihedral : 4.126 32.829 485 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.61 % Allowed : 18.98 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.42), residues: 415 helix: 1.70 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -0.83 (0.97), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 178 HIS 0.005 0.001 HIS A 341 PHE 0.018 0.002 PHE A 410 TYR 0.012 0.001 TYR A 339 ARG 0.002 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Evaluate side-chains 82 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 ARG cc_start: 0.7608 (ttp-170) cc_final: 0.7402 (ttm-80) REVERT: A 242 SER cc_start: 0.8287 (p) cc_final: 0.8080 (m) REVERT: A 389 ARG cc_start: 0.6623 (OUTLIER) cc_final: 0.5827 (mtp180) outliers start: 12 outliers final: 8 residues processed: 75 average time/residue: 1.7772 time to fit residues: 138.6756 Evaluate side-chains 79 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 536 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 0.4980 chunk 37 optimal weight: 0.1980 chunk 41 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 chunk 14 optimal weight: 0.1980 chunk 28 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 overall best weight: 0.3580 ------------------------------------------------------------------------------- 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 = 0.4112 r_free = 0.4112 target = 0.157595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.145685 restraints weight = 13429.738| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 1.76 r_work: 0.3907 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3789 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3291 Z= 0.256 Angle : 0.536 5.613 4471 Z= 0.287 Chirality : 0.037 0.134 531 Planarity : 0.005 0.050 544 Dihedral : 4.053 31.284 485 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.01 % Allowed : 19.28 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.42), residues: 415 helix: 1.82 (0.27), residues: 367 sheet: None (None), residues: 0 loop : -0.84 (0.93), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 178 HIS 0.005 0.001 HIS A 341 PHE 0.017 0.002 PHE A 410 TYR 0.014 0.001 TYR A 339 ARG 0.002 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Evaluate side-chains 79 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 ARG cc_start: 0.7614 (ttp-170) cc_final: 0.7413 (ttm-80) REVERT: A 242 SER cc_start: 0.8286 (p) cc_final: 0.8072 (m) REVERT: A 390 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.7051 (tt) outliers start: 10 outliers final: 7 residues processed: 72 average time/residue: 1.9152 time to fit residues: 143.5224 Evaluate side-chains 77 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 536 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 0.0980 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 22 optimal weight: 0.2980 chunk 39 optimal weight: 0.0970 chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 0.0980 chunk 14 optimal weight: 0.0770 overall best weight: 0.1336 ------------------------------------------------------------------------------- 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 = 0.4146 r_free = 0.4146 target = 0.160515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.148622 restraints weight = 13449.357| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 1.79 r_work: 0.3942 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3823 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3291 Z= 0.165 Angle : 0.503 6.001 4471 Z= 0.264 Chirality : 0.036 0.126 531 Planarity : 0.004 0.051 544 Dihedral : 3.769 24.997 485 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.11 % Allowed : 20.18 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.42), residues: 415 helix: 2.08 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -0.61 (1.00), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 178 HIS 0.003 0.001 HIS A 341 PHE 0.012 0.001 PHE A 410 TYR 0.011 0.001 TYR A 339 ARG 0.002 0.000 ARG A 264 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Evaluate side-chains 77 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 ARG cc_start: 0.7576 (ttp-170) cc_final: 0.7375 (ttm-80) REVERT: A 242 SER cc_start: 0.8093 (p) cc_final: 0.7866 (m) REVERT: A 261 TRP cc_start: 0.7368 (m100) cc_final: 0.6298 (m100) REVERT: A 390 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.7054 (tt) outliers start: 7 outliers final: 4 residues processed: 74 average time/residue: 1.8431 time to fit residues: 141.8277 Evaluate side-chains 74 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 470 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 30 optimal weight: 0.4980 chunk 8 optimal weight: 0.2980 chunk 1 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 7 optimal weight: 0.0980 chunk 16 optimal weight: 0.0870 chunk 15 optimal weight: 0.9990 overall best weight: 0.3758 ------------------------------------------------------------------------------- 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 = 0.4117 r_free = 0.4117 target = 0.157644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.145759 restraints weight = 13595.100| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 1.81 r_work: 0.3909 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3788 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3291 Z= 0.263 Angle : 0.538 5.505 4471 Z= 0.290 Chirality : 0.037 0.136 531 Planarity : 0.005 0.049 544 Dihedral : 3.954 29.506 485 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.41 % Allowed : 21.08 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.42), residues: 415 helix: 1.97 (0.27), residues: 367 sheet: None (None), residues: 0 loop : -0.84 (0.95), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 178 HIS 0.006 0.001 HIS A 341 PHE 0.017 0.002 PHE A 410 TYR 0.012 0.001 TYR A 339 ARG 0.002 0.000 ARG A 264 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6185.34 seconds wall clock time: 105 minutes 18.60 seconds (6318.60 seconds total)