Starting phenix.real_space_refine on Wed Mar 5 16:56:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t69_41066/03_2025/8t69_41066.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t69_41066/03_2025/8t69_41066.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t69_41066/03_2025/8t69_41066.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t69_41066/03_2025/8t69_41066.map" model { file = "/net/cci-nas-00/data/ceres_data/8t69_41066/03_2025/8t69_41066.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t69_41066/03_2025/8t69_41066.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.032 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 28 5.16 5 C 1950 2.51 5 N 450 2.21 5 O 495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 2923 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 2900 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 23, 'TRANS': 362} Chain breaks: 1 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'YHL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.07, per 1000 atoms: 1.05 Number of scatterers: 2923 At special positions: 0 Unit cell: (70.741, 62.304, 64.251, 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 28 16.00 O 495 8.00 N 450 7.00 C 1950 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 425.1 milliseconds 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 696 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 90.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 19 through 39 Processing helix chain 'A' and resid 43 through 49 removed outlier: 3.740A pdb=" N TYR A 47 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 48 " --> pdb=" O ILE A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 157 removed outlier: 4.391A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 3.961A pdb=" N ASN A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 178 removed outlier: 3.734A pdb=" N PHE A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 211 removed outlier: 4.156A pdb=" N GLY A 203 " --> pdb=" O SER A 199 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N MET A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 246 Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 249 through 271 Processing helix chain 'A' and resid 284 through 290 Processing helix chain 'A' and resid 291 through 312 removed outlier: 3.802A pdb=" N ASN A 305 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET A 306 " --> pdb=" O CYS A 302 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLY A 307 " --> pdb=" O PHE A 303 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 Proline residue: A 316 - end of helix No H-bonds generated for 'chain 'A' and resid 313 through 318' Processing helix chain 'A' and resid 319 through 325 removed outlier: 3.755A pdb=" N MET A 323 " --> pdb=" O MET A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 333 removed outlier: 4.082A pdb=" N GLY A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 356 removed outlier: 4.191A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N HIS A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 374 Processing helix chain 'A' and resid 375 through 378 Processing helix chain 'A' and resid 380 through 383 Processing helix chain 'A' and resid 384 through 414 Proline residue: A 404 - end of helix removed outlier: 3.939A pdb=" N GLY A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 410 " --> pdb=" O MET A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 447 removed outlier: 4.137A pdb=" N GLY A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) Proline residue: A 437 - end of helix removed outlier: 4.193A pdb=" N GLY A 441 " --> pdb=" O PRO A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 465 through 471 236 hydrogen bonds defined for protein. 690 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: 0.83 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 511 1.33 - 1.45: 707 1.45 - 1.57: 1728 1.57 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 2994 Sorted by residual: bond pdb=" C16 YHL A 901 " pdb=" N7 YHL A 901 " ideal model delta sigma weight residual 1.445 1.510 -0.065 2.00e-02 2.50e+03 1.04e+01 bond pdb=" C6 YHL A 901 " pdb=" N7 YHL A 901 " ideal model delta sigma weight residual 1.443 1.503 -0.060 2.00e-02 2.50e+03 9.06e+00 bond pdb=" C8 YHL A 901 " pdb=" N7 YHL A 901 " ideal model delta sigma weight residual 1.451 1.503 -0.052 2.00e-02 2.50e+03 6.68e+00 bond pdb=" C ILE A 375 " pdb=" N PRO A 376 " ideal model delta sigma weight residual 1.335 1.360 -0.026 1.19e-02 7.06e+03 4.73e+00 bond pdb=" C5 YHL A 901 " pdb=" C6 YHL A 901 " ideal model delta sigma weight residual 1.550 1.523 0.027 2.00e-02 2.50e+03 1.78e+00 ... (remaining 2989 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 3941 1.51 - 3.02: 99 3.02 - 4.54: 22 4.54 - 6.05: 9 6.05 - 7.56: 3 Bond angle restraints: 4074 Sorted by residual: angle pdb=" N TYR A 158 " pdb=" CA TYR A 158 " pdb=" C TYR A 158 " ideal model delta sigma weight residual 109.81 117.37 -7.56 2.21e+00 2.05e-01 1.17e+01 angle pdb=" C CYS A 374 " pdb=" N ILE A 375 " pdb=" CA ILE A 375 " ideal model delta sigma weight residual 120.33 122.97 -2.64 8.00e-01 1.56e+00 1.09e+01 angle pdb=" C ILE A 435 " pdb=" N GLY A 436 " pdb=" CA GLY A 436 " ideal model delta sigma weight residual 121.13 123.23 -2.10 7.30e-01 1.88e+00 8.28e+00 angle pdb=" C PHE A 245 " pdb=" N VAL A 246 " pdb=" CA VAL A 246 " ideal model delta sigma weight residual 123.16 120.46 2.70 1.06e+00 8.90e-01 6.46e+00 angle pdb=" N PRO A 236 " pdb=" CA PRO A 236 " pdb=" C PRO A 236 " ideal model delta sigma weight residual 110.70 113.71 -3.01 1.22e+00 6.72e-01 6.09e+00 ... (remaining 4069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.55: 1600 12.55 - 25.10: 135 25.10 - 37.65: 34 37.65 - 50.20: 8 50.20 - 62.76: 1 Dihedral angle restraints: 1778 sinusoidal: 685 harmonic: 1093 Sorted by residual: dihedral pdb=" CA VAL A 417 " pdb=" C VAL A 417 " pdb=" N TYR A 418 " pdb=" CA TYR A 418 " ideal model delta harmonic sigma weight residual -180.00 -159.60 -20.40 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA VAL A 332 " pdb=" C VAL A 332 " pdb=" N ALA A 333 " pdb=" CA ALA A 333 " ideal model delta harmonic sigma weight residual 180.00 -161.38 -18.62 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA SER A 401 " pdb=" C SER A 401 " pdb=" N MET A 402 " pdb=" CA MET A 402 " ideal model delta harmonic sigma weight residual -180.00 -163.78 -16.22 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 1775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 348 0.042 - 0.084: 101 0.084 - 0.127: 33 0.127 - 0.169: 2 0.169 - 0.211: 1 Chirality restraints: 485 Sorted by residual: chirality pdb=" C16 YHL A 901 " pdb=" C15 YHL A 901 " pdb=" C17 YHL A 901 " pdb=" N7 YHL A 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" C5 YHL A 901 " pdb=" C18 YHL A 901 " pdb=" C4 YHL A 901 " pdb=" C6 YHL A 901 " both_signs ideal model delta sigma weight residual False 2.54 2.70 -0.16 2.00e-01 2.50e+01 6.08e-01 chirality pdb=" CA TYR A 158 " pdb=" N TYR A 158 " pdb=" C TYR A 158 " pdb=" CB TYR A 158 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 482 not shown) Planarity restraints: 498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 436 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.60e+00 pdb=" N PRO A 437 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 437 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 437 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 235 " -0.030 5.00e-02 4.00e+02 4.52e-02 3.28e+00 pdb=" N PRO A 236 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 236 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 236 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 202 " 0.007 2.00e-02 2.50e+03 1.41e-02 1.99e+00 pdb=" C ALA A 202 " -0.024 2.00e-02 2.50e+03 pdb=" O ALA A 202 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY A 203 " 0.008 2.00e-02 2.50e+03 ... (remaining 495 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 1061 2.88 - 3.39: 3156 3.39 - 3.89: 4993 3.89 - 4.40: 5728 4.40 - 4.90: 9896 Nonbonded interactions: 24834 Sorted by model distance: nonbonded pdb=" OD1 ASP A 411 " pdb=" OG SER A 416 " model vdw 2.381 3.040 nonbonded pdb=" OH TYR A 47 " pdb=" O SER A 179 " model vdw 2.388 3.040 nonbonded pdb=" O MET A 397 " pdb=" OG SER A 401 " model vdw 2.424 3.040 nonbonded pdb=" O TYR A 341 " pdb=" OG1 THR A 345 " model vdw 2.428 3.040 nonbonded pdb=" OH TYR A 341 " pdb=" OD2 ASP A 399 " model vdw 2.449 3.040 ... (remaining 24829 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: 2.540 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.010 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:13.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 2994 Z= 0.238 Angle : 0.670 7.561 4074 Z= 0.359 Chirality : 0.044 0.211 485 Planarity : 0.006 0.047 498 Dihedral : 10.446 62.755 1082 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.64 % Allowed : 3.22 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.45), residues: 382 helix: 1.02 (0.31), residues: 296 sheet: None (None), residues: 0 loop : 0.11 (0.75), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 318 HIS 0.002 0.001 HIS A 414 PHE 0.016 0.002 PHE A 238 TYR 0.017 0.001 TYR A 422 ARG 0.003 0.001 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.317 Fit side-chains REVERT: A 33 ASP cc_start: 0.7044 (t0) cc_final: 0.6738 (t0) REVERT: A 319 MET cc_start: 0.6211 (mtm) cc_final: 0.5653 (mmp) REVERT: A 403 MET cc_start: 0.8573 (mmm) cc_final: 0.8127 (mmm) outliers start: 2 outliers final: 0 residues processed: 59 average time/residue: 0.8758 time to fit residues: 53.7330 Evaluate side-chains 43 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3697 r_free = 0.3697 target = 0.155163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.141021 restraints weight = 3175.183| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.03 r_work: 0.3425 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2994 Z= 0.262 Angle : 0.668 6.663 4074 Z= 0.337 Chirality : 0.044 0.152 485 Planarity : 0.006 0.047 498 Dihedral : 5.014 22.586 439 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.89 % Allowed : 8.04 % Favored : 89.07 % 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: 1.58 (0.45), residues: 382 helix: 1.35 (0.31), residues: 301 sheet: None (None), residues: 0 loop : 0.20 (0.73), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 451 HIS 0.002 0.001 HIS A 353 PHE 0.016 0.002 PHE A 176 TYR 0.015 0.002 TYR A 422 ARG 0.003 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.278 Fit side-chains REVERT: A 33 ASP cc_start: 0.6821 (t0) cc_final: 0.6566 (t0) REVERT: A 169 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7559 (tpp) REVERT: A 319 MET cc_start: 0.6424 (mtm) cc_final: 0.5831 (mmp) outliers start: 9 outliers final: 5 residues processed: 51 average time/residue: 0.9615 time to fit residues: 50.7740 Evaluate side-chains 48 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 372 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 34 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 15 optimal weight: 0.0770 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 37 optimal weight: 0.0670 overall best weight: 0.4476 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.158504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.142969 restraints weight = 3089.839| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.15 r_work: 0.3491 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2994 Z= 0.192 Angle : 0.583 6.730 4074 Z= 0.296 Chirality : 0.041 0.129 485 Planarity : 0.006 0.047 498 Dihedral : 4.581 17.482 439 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.57 % Allowed : 9.65 % Favored : 87.78 % 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: 1.92 (0.45), residues: 382 helix: 1.60 (0.31), residues: 307 sheet: None (None), residues: 0 loop : 0.12 (0.79), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 358 HIS 0.001 0.001 HIS A 414 PHE 0.012 0.001 PHE A 27 TYR 0.013 0.001 TYR A 422 ARG 0.001 0.000 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.310 Fit side-chains REVERT: A 33 ASP cc_start: 0.6815 (t0) cc_final: 0.6583 (t0) REVERT: A 169 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7527 (tpp) REVERT: A 319 MET cc_start: 0.6589 (mtm) cc_final: 0.6043 (mmp) outliers start: 8 outliers final: 3 residues processed: 48 average time/residue: 1.0045 time to fit residues: 49.9113 Evaluate side-chains 45 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 332 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 10 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 2 optimal weight: 0.0060 chunk 1 optimal weight: 0.6980 chunk 32 optimal weight: 0.0170 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.4634 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.157952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.140207 restraints weight = 3147.095| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.39 r_work: 0.3504 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2994 Z= 0.197 Angle : 0.580 6.774 4074 Z= 0.293 Chirality : 0.041 0.135 485 Planarity : 0.006 0.046 498 Dihedral : 4.406 18.021 439 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.57 % Allowed : 8.68 % Favored : 88.75 % 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: 2.02 (0.45), residues: 382 helix: 1.76 (0.31), residues: 306 sheet: None (None), residues: 0 loop : -0.24 (0.74), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 358 HIS 0.001 0.001 HIS A 353 PHE 0.013 0.001 PHE A 238 TYR 0.017 0.001 TYR A 422 ARG 0.002 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.323 Fit side-chains REVERT: A 33 ASP cc_start: 0.6698 (t0) cc_final: 0.6395 (t0) REVERT: A 169 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7413 (tpp) REVERT: A 276 GLN cc_start: 0.6291 (OUTLIER) cc_final: 0.5756 (mt0) REVERT: A 319 MET cc_start: 0.6524 (mtm) cc_final: 0.5870 (mmp) outliers start: 8 outliers final: 4 residues processed: 47 average time/residue: 1.0311 time to fit residues: 50.1137 Evaluate side-chains 47 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 332 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 21 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 36 optimal weight: 0.0670 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 = 0.3728 r_free = 0.3728 target = 0.156681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.139229 restraints weight = 3135.749| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.35 r_work: 0.3471 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2994 Z= 0.209 Angle : 0.581 6.794 4074 Z= 0.293 Chirality : 0.042 0.137 485 Planarity : 0.006 0.046 498 Dihedral : 4.363 17.432 439 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.89 % Allowed : 9.32 % Favored : 87.78 % 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 (0.45), residues: 382 helix: 1.74 (0.31), residues: 309 sheet: None (None), residues: 0 loop : -0.29 (0.76), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 358 HIS 0.001 0.000 HIS A 353 PHE 0.013 0.001 PHE A 238 TYR 0.017 0.001 TYR A 422 ARG 0.002 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.309 Fit side-chains REVERT: A 33 ASP cc_start: 0.6766 (t0) cc_final: 0.6469 (t0) REVERT: A 169 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.6768 (tpt) REVERT: A 276 GLN cc_start: 0.6391 (OUTLIER) cc_final: 0.5910 (mt0) REVERT: A 319 MET cc_start: 0.6624 (mtm) cc_final: 0.6031 (mmp) outliers start: 9 outliers final: 5 residues processed: 46 average time/residue: 0.9979 time to fit residues: 47.5001 Evaluate side-chains 48 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 332 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 5 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 6 optimal weight: 0.3980 chunk 3 optimal weight: 0.1980 chunk 2 optimal weight: 0.0470 chunk 37 optimal weight: 1.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.158594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.139282 restraints weight = 3171.900| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.57 r_work: 0.3493 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2994 Z= 0.189 Angle : 0.560 6.721 4074 Z= 0.283 Chirality : 0.041 0.132 485 Planarity : 0.006 0.046 498 Dihedral : 4.261 17.109 439 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.22 % Allowed : 9.65 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.45), residues: 382 helix: 1.75 (0.31), residues: 314 sheet: None (None), residues: 0 loop : -0.47 (0.81), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 358 HIS 0.001 0.000 HIS A 353 PHE 0.012 0.001 PHE A 238 TYR 0.017 0.001 TYR A 422 ARG 0.002 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.325 Fit side-chains REVERT: A 33 ASP cc_start: 0.6479 (t0) cc_final: 0.6169 (t0) REVERT: A 35 MET cc_start: 0.8705 (ttm) cc_final: 0.8424 (mtp) REVERT: A 169 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.6461 (tpt) REVERT: A 230 MET cc_start: 0.7543 (mmm) cc_final: 0.7321 (tpt) REVERT: A 276 GLN cc_start: 0.6015 (OUTLIER) cc_final: 0.5574 (mt0) REVERT: A 319 MET cc_start: 0.6533 (mtm) cc_final: 0.5849 (mmp) outliers start: 10 outliers final: 6 residues processed: 48 average time/residue: 0.8974 time to fit residues: 44.7167 Evaluate side-chains 48 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 332 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 6 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3757 r_free = 0.3757 target = 0.156773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.138043 restraints weight = 3194.023| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.59 r_work: 0.3520 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2994 Z= 0.249 Angle : 0.604 6.859 4074 Z= 0.304 Chirality : 0.043 0.144 485 Planarity : 0.006 0.048 498 Dihedral : 4.405 18.255 439 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.54 % Allowed : 9.97 % Favored : 86.50 % 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: 1.79 (0.45), residues: 382 helix: 1.63 (0.30), residues: 314 sheet: None (None), residues: 0 loop : -0.76 (0.79), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 358 HIS 0.001 0.000 HIS A 353 PHE 0.014 0.002 PHE A 238 TYR 0.019 0.001 TYR A 422 ARG 0.002 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.307 Fit side-chains REVERT: A 33 ASP cc_start: 0.6440 (t0) cc_final: 0.6104 (t0) REVERT: A 169 MET cc_start: 0.7197 (OUTLIER) cc_final: 0.6414 (tpt) REVERT: A 276 GLN cc_start: 0.6007 (OUTLIER) cc_final: 0.5567 (mt0) REVERT: A 310 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7573 (mmt) REVERT: A 319 MET cc_start: 0.6575 (mtm) cc_final: 0.5863 (mmp) outliers start: 11 outliers final: 6 residues processed: 49 average time/residue: 1.0210 time to fit residues: 51.7692 Evaluate side-chains 50 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 12 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.167687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.148921 restraints weight = 3153.685| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.55 r_work: 0.3610 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2994 Z= 0.245 Angle : 0.597 6.809 4074 Z= 0.302 Chirality : 0.043 0.143 485 Planarity : 0.006 0.047 498 Dihedral : 4.402 18.154 439 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.86 % Allowed : 9.97 % Favored : 86.17 % 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: 1.69 (0.45), residues: 382 helix: 1.59 (0.30), residues: 314 sheet: None (None), residues: 0 loop : -0.99 (0.78), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 358 HIS 0.001 0.000 HIS A 353 PHE 0.013 0.001 PHE A 238 TYR 0.019 0.001 TYR A 422 ARG 0.002 0.001 ARG A 471 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.312 Fit side-chains REVERT: A 33 ASP cc_start: 0.7126 (t0) cc_final: 0.6793 (t0) REVERT: A 169 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7132 (tpt) REVERT: A 230 MET cc_start: 0.8037 (mmm) cc_final: 0.7833 (tpt) REVERT: A 276 GLN cc_start: 0.6479 (OUTLIER) cc_final: 0.6005 (mt0) REVERT: A 310 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.8036 (mmt) REVERT: A 319 MET cc_start: 0.7025 (mtm) cc_final: 0.6411 (mmp) outliers start: 12 outliers final: 7 residues processed: 46 average time/residue: 0.9827 time to fit residues: 46.8353 Evaluate side-chains 50 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 10 optimal weight: 0.7980 chunk 24 optimal weight: 0.4980 chunk 31 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.169818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.151178 restraints weight = 3165.612| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 1.55 r_work: 0.3639 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2994 Z= 0.196 Angle : 0.561 6.749 4074 Z= 0.285 Chirality : 0.041 0.134 485 Planarity : 0.006 0.047 498 Dihedral : 4.255 17.336 439 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.86 % Allowed : 9.97 % Favored : 86.17 % 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: 1.91 (0.45), residues: 382 helix: 1.75 (0.31), residues: 314 sheet: None (None), residues: 0 loop : -0.97 (0.78), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 358 HIS 0.001 0.000 HIS A 353 PHE 0.012 0.001 PHE A 238 TYR 0.017 0.001 TYR A 422 ARG 0.002 0.000 ARG A 471 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.319 Fit side-chains REVERT: A 33 ASP cc_start: 0.7048 (t0) cc_final: 0.6725 (t0) REVERT: A 35 MET cc_start: 0.9012 (ttm) cc_final: 0.8762 (mtp) REVERT: A 169 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7112 (tpt) REVERT: A 276 GLN cc_start: 0.6431 (OUTLIER) cc_final: 0.5963 (mt0) REVERT: A 310 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.8020 (mmt) REVERT: A 319 MET cc_start: 0.7019 (mtm) cc_final: 0.6426 (mmp) outliers start: 12 outliers final: 6 residues processed: 47 average time/residue: 0.9873 time to fit residues: 48.0592 Evaluate side-chains 50 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 332 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 26 optimal weight: 0.0370 chunk 15 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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 = 0.3956 r_free = 0.3956 target = 0.169803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.151335 restraints weight = 3186.858| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 1.54 r_work: 0.3643 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2994 Z= 0.199 Angle : 0.566 6.744 4074 Z= 0.287 Chirality : 0.041 0.138 485 Planarity : 0.006 0.047 498 Dihedral : 4.246 17.351 439 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.54 % Allowed : 10.29 % Favored : 86.17 % 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: 1.93 (0.45), residues: 382 helix: 1.77 (0.31), residues: 314 sheet: None (None), residues: 0 loop : -0.97 (0.79), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 358 HIS 0.001 0.000 HIS A 353 PHE 0.015 0.001 PHE A 238 TYR 0.017 0.001 TYR A 422 ARG 0.004 0.001 ARG A 471 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.327 Fit side-chains REVERT: A 33 ASP cc_start: 0.7059 (t0) cc_final: 0.6728 (t0) REVERT: A 35 MET cc_start: 0.9012 (ttm) cc_final: 0.8770 (mtp) REVERT: A 169 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7103 (tpt) REVERT: A 276 GLN cc_start: 0.6452 (OUTLIER) cc_final: 0.5967 (mt0) REVERT: A 310 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.8040 (mmt) REVERT: A 319 MET cc_start: 0.7045 (mtm) cc_final: 0.6434 (mmp) outliers start: 11 outliers final: 7 residues processed: 49 average time/residue: 0.9816 time to fit residues: 49.8204 Evaluate side-chains 52 residues out of total 311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 6 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3926 r_free = 0.3926 target = 0.167204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.148761 restraints weight = 3133.980| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.54 r_work: 0.3610 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2994 Z= 0.264 Angle : 0.612 6.864 4074 Z= 0.310 Chirality : 0.043 0.148 485 Planarity : 0.006 0.047 498 Dihedral : 4.390 16.849 439 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.22 % Allowed : 10.93 % Favored : 85.85 % 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: 1.68 (0.45), residues: 382 helix: 1.61 (0.30), residues: 314 sheet: None (None), residues: 0 loop : -1.15 (0.77), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 358 HIS 0.001 0.000 HIS A 353 PHE 0.017 0.002 PHE A 238 TYR 0.020 0.002 TYR A 422 ARG 0.005 0.001 ARG A 471 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2419.56 seconds wall clock time: 41 minutes 59.89 seconds (2519.89 seconds total)