Starting phenix.real_space_refine on Wed Mar 12 14:25:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kdt_22829/03_2025/7kdt_22829.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kdt_22829/03_2025/7kdt_22829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kdt_22829/03_2025/7kdt_22829.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kdt_22829/03_2025/7kdt_22829.map" model { file = "/net/cci-nas-00/data/ceres_data/7kdt_22829/03_2025/7kdt_22829.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kdt_22829/03_2025/7kdt_22829.cif" } resolution = 3.05 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= 0.105 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 27 5.16 5 C 2543 2.51 5 N 683 2.21 5 O 769 1.98 5 H 4042 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 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: 8064 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 7444 Classifications: {'peptide': 467} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 454} Chain breaks: 1 Chain: "B" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 620 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 3, 'TRANS': 34} Time building chain proxies: 4.12, per 1000 atoms: 0.51 Number of scatterers: 8064 At special positions: 0 Unit cell: (57.546, 70.89, 115.926, 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 27 16.00 O 769 8.00 N 683 7.00 C 2543 6.00 H 4042 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: 2.15 Conformation dependent library (CDL) restraints added in 765.1 milliseconds 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 976 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 0 sheets defined 85.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 109 through 127 removed outlier: 4.286A pdb=" N ALA A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 144 Processing helix chain 'A' and resid 145 through 149 Processing helix chain 'A' and resid 152 through 166 removed outlier: 3.708A pdb=" N ALA A 162 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE A 163 " --> pdb=" O ARG A 159 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 183 Processing helix chain 'A' and resid 186 through 200 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 221 through 245 removed outlier: 3.571A pdb=" N GLU A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 262 Processing helix chain 'A' and resid 299 through 307 removed outlier: 4.360A pdb=" N GLN A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TYR A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 311 No H-bonds generated for 'chain 'A' and resid 309 through 311' Processing helix chain 'A' and resid 312 through 321 removed outlier: 3.501A pdb=" N LYS A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 343 removed outlier: 6.115A pdb=" N GLU A 330 " --> pdb=" O LYS A 326 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LEU A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 358 Proline residue: A 350 - end of helix removed outlier: 3.595A pdb=" N VAL A 355 " --> pdb=" O ASP A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 380 Processing helix chain 'A' and resid 382 through 397 removed outlier: 3.624A pdb=" N ALA A 394 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 414 removed outlier: 3.809A pdb=" N TYR A 404 " --> pdb=" O ASN A 400 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 413 " --> pdb=" O GLN A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 431 removed outlier: 3.521A pdb=" N ALA A 420 " --> pdb=" O GLN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 452 removed outlier: 3.653A pdb=" N GLN A 438 " --> pdb=" O SER A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 472 removed outlier: 3.816A pdb=" N GLU A 466 " --> pdb=" O MET A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 489 Processing helix chain 'A' and resid 491 through 506 removed outlier: 3.514A pdb=" N GLU A 497 " --> pdb=" O GLY A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 521 removed outlier: 4.136A pdb=" N TYR A 513 " --> pdb=" O ASN A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 541 removed outlier: 3.881A pdb=" N GLU A 532 " --> pdb=" O ASP A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 558 Processing helix chain 'A' and resid 560 through 573 Processing helix chain 'A' and resid 577 through 599 removed outlier: 3.688A pdb=" N HIS A 583 " --> pdb=" O MET A 579 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 587 " --> pdb=" O HIS A 583 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS A 599 " --> pdb=" O THR A 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 69 removed outlier: 4.876A pdb=" N SER B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 64 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 76 290 hydrogen bonds defined for protein. 858 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: 2.89 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.06: 1022 1.06 - 1.25: 3587 1.25 - 1.44: 1110 1.44 - 1.63: 2367 1.63 - 1.82: 42 Bond restraints: 8128 Sorted by residual: bond pdb=" C GLN A 115 " pdb=" O GLN A 115 " ideal model delta sigma weight residual 1.236 1.141 0.095 1.15e-02 7.56e+03 6.85e+01 bond pdb=" N GLU A 549 " pdb=" H GLU A 549 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" CD1 TYR A 479 " pdb=" HD1 TYR A 479 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" CD1 PHE A 390 " pdb=" HD1 PHE A 390 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" CD1 TYR A 304 " pdb=" HD1 TYR A 304 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.62e+01 ... (remaining 8123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 12596 2.65 - 5.29: 1638 5.29 - 7.94: 467 7.94 - 10.58: 19 10.58 - 13.23: 10 Bond angle restraints: 14730 Sorted by residual: angle pdb=" CA GLN A 115 " pdb=" C GLN A 115 " pdb=" O GLN A 115 " ideal model delta sigma weight residual 120.82 114.53 6.29 1.05e+00 9.07e-01 3.58e+01 angle pdb=" CA GLN A 132 " pdb=" C GLN A 132 " pdb=" O GLN A 132 " ideal model delta sigma weight residual 120.42 114.45 5.97 1.06e+00 8.90e-01 3.18e+01 angle pdb=" N GLN A 416 " pdb=" CA GLN A 416 " pdb=" C GLN A 416 " ideal model delta sigma weight residual 109.62 102.09 7.53 1.50e+00 4.44e-01 2.52e+01 angle pdb=" C LYS A 516 " pdb=" N GLY A 517 " pdb=" CA GLY A 517 " ideal model delta sigma weight residual 119.94 125.39 -5.45 1.09e+00 8.42e-01 2.50e+01 angle pdb=" CA LYS A 349 " pdb=" C LYS A 349 " pdb=" O LYS A 349 " ideal model delta sigma weight residual 118.33 113.80 4.53 9.20e-01 1.18e+00 2.43e+01 ... (remaining 14725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 3508 17.70 - 35.41: 182 35.41 - 53.11: 47 53.11 - 70.81: 47 70.81 - 88.52: 21 Dihedral angle restraints: 3805 sinusoidal: 2092 harmonic: 1713 Sorted by residual: dihedral pdb=" CA GLU A 320 " pdb=" C GLU A 320 " pdb=" N ILE A 321 " pdb=" CA ILE A 321 " ideal model delta harmonic sigma weight residual 180.00 151.67 28.33 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA LEU B 46 " pdb=" C LEU B 46 " pdb=" N ARG B 47 " pdb=" CA ARG B 47 " ideal model delta harmonic sigma weight residual 180.00 152.02 27.98 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA THR A 451 " pdb=" C THR A 451 " pdb=" N GLY A 452 " pdb=" CA GLY A 452 " ideal model delta harmonic sigma weight residual 180.00 154.55 25.45 0 5.00e+00 4.00e-02 2.59e+01 ... (remaining 3802 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 342 0.063 - 0.127: 181 0.127 - 0.190: 51 0.190 - 0.253: 22 0.253 - 0.316: 6 Chirality restraints: 602 Sorted by residual: chirality pdb=" CA GLU A 308 " pdb=" N GLU A 308 " pdb=" C GLU A 308 " pdb=" CB GLU A 308 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CA PHE A 219 " pdb=" N PHE A 219 " pdb=" C PHE A 219 " pdb=" CB PHE A 219 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA ARG A 529 " pdb=" N ARG A 529 " pdb=" C ARG A 529 " pdb=" CB ARG A 529 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 599 not shown) Planarity restraints: 1201 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 520 " 0.056 2.00e-02 2.50e+03 4.40e-01 2.91e+03 pdb=" CD GLN A 520 " -0.018 2.00e-02 2.50e+03 pdb=" OE1 GLN A 520 " -0.052 2.00e-02 2.50e+03 pdb=" NE2 GLN A 520 " 0.000 2.00e-02 2.50e+03 pdb="HE21 GLN A 520 " 0.768 2.00e-02 2.50e+03 pdb="HE22 GLN A 520 " -0.754 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 115 " 0.078 2.00e-02 2.50e+03 4.36e-01 2.85e+03 pdb=" CD GLN A 115 " 0.007 2.00e-02 2.50e+03 pdb=" OE1 GLN A 115 " -0.084 2.00e-02 2.50e+03 pdb=" NE2 GLN A 115 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN A 115 " -0.753 2.00e-02 2.50e+03 pdb="HE22 GLN A 115 " 0.748 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 220 " 0.119 2.00e-02 2.50e+03 4.33e-01 2.82e+03 pdb=" CD GLN A 220 " -0.011 2.00e-02 2.50e+03 pdb=" OE1 GLN A 220 " -0.115 2.00e-02 2.50e+03 pdb=" NE2 GLN A 220 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN A 220 " 0.745 2.00e-02 2.50e+03 pdb="HE22 GLN A 220 " -0.738 2.00e-02 2.50e+03 ... (remaining 1198 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 413 2.20 - 2.80: 15423 2.80 - 3.40: 23181 3.40 - 4.00: 29503 4.00 - 4.60: 44103 Nonbonded interactions: 112623 Sorted by model distance: nonbonded pdb=" OD2 ASP A 267 " pdb=" HG SER A 270 " model vdw 1.603 2.450 nonbonded pdb=" OE1 GLU A 217 " pdb=" HG SER A 224 " model vdw 1.611 2.450 nonbonded pdb=" OD1 ASP A 151 " pdb=" HG SER A 153 " model vdw 1.625 2.450 nonbonded pdb=" O ALA A 483 " pdb=" HG1 THR A 487 " model vdw 1.654 2.450 nonbonded pdb=" OD1 ASN A 509 " pdb=" HG1 THR A 512 " model vdw 1.663 2.450 ... (remaining 112618 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.030 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: 0.120 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.330 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 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 : 0.012 0.095 4086 Z= 0.778 Angle : 1.742 7.528 5493 Z= 1.206 Chirality : 0.088 0.316 602 Planarity : 0.018 0.193 714 Dihedral : 14.556 88.516 1574 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 0.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.47 % Allowed : 1.17 % Favored : 98.37 % 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: -1.64 (0.32), residues: 499 helix: -0.92 (0.21), residues: 405 sheet: None (None), residues: 0 loop : -0.95 (0.65), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.018 TRP A 523 HIS 0.012 0.004 HIS A 405 PHE 0.070 0.015 PHE A 191 TYR 0.171 0.021 TYR A 186 ARG 0.009 0.002 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 122 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.8506 (tttp) cc_final: 0.8177 (mtpt) outliers start: 2 outliers final: 0 residues processed: 123 average time/residue: 0.4316 time to fit residues: 63.1711 Evaluate side-chains 72 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN A 409 GLN A 515 HIS A 520 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.152319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.127673 restraints weight = 15773.608| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.54 r_work: 0.3562 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4086 Z= 0.198 Angle : 0.599 5.489 5493 Z= 0.328 Chirality : 0.035 0.133 602 Planarity : 0.005 0.055 714 Dihedral : 4.971 23.859 542 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.93 % Allowed : 6.76 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.36), residues: 499 helix: 0.97 (0.24), residues: 413 sheet: None (None), residues: 0 loop : -0.77 (0.61), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 169 HIS 0.004 0.002 HIS A 405 PHE 0.020 0.002 PHE A 465 TYR 0.023 0.002 TYR A 186 ARG 0.004 0.001 ARG A 529 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 GLU cc_start: 0.8243 (mt-10) cc_final: 0.8019 (tm-30) REVERT: A 392 MET cc_start: 0.7681 (mmp) cc_final: 0.7373 (tpt) REVERT: A 425 ASP cc_start: 0.8444 (t0) cc_final: 0.8155 (m-30) REVERT: A 462 MET cc_start: 0.7198 (mmt) cc_final: 0.6933 (mmt) REVERT: B 59 LYS cc_start: 0.8217 (tttp) cc_final: 0.8010 (mtpt) outliers start: 4 outliers final: 3 residues processed: 84 average time/residue: 0.3515 time to fit residues: 37.6097 Evaluate side-chains 72 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 60 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 31 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3951 r_free = 0.3951 target = 0.151486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.125593 restraints weight = 16292.328| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.71 r_work: 0.3535 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4086 Z= 0.177 Angle : 0.517 4.081 5493 Z= 0.281 Chirality : 0.033 0.120 602 Planarity : 0.003 0.046 714 Dihedral : 4.407 20.635 542 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.17 % Allowed : 7.23 % Favored : 91.61 % 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: 1.80 (0.37), residues: 499 helix: 1.55 (0.25), residues: 417 sheet: None (None), residues: 0 loop : -0.44 (0.69), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 169 HIS 0.004 0.002 HIS A 405 PHE 0.020 0.002 PHE A 163 TYR 0.013 0.001 TYR A 186 ARG 0.002 0.000 ARG A 529 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 391 ASN cc_start: 0.7748 (m-40) cc_final: 0.7302 (p0) REVERT: A 425 ASP cc_start: 0.8306 (t0) cc_final: 0.7986 (m-30) REVERT: A 462 MET cc_start: 0.7073 (mmt) cc_final: 0.6760 (mmt) outliers start: 5 outliers final: 3 residues processed: 74 average time/residue: 0.3579 time to fit residues: 33.0614 Evaluate side-chains 66 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain B residue 60 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 44 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 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 = 0.3949 r_free = 0.3949 target = 0.151366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.125969 restraints weight = 16190.668| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.61 r_work: 0.3547 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4086 Z= 0.150 Angle : 0.475 4.873 5493 Z= 0.254 Chirality : 0.033 0.126 602 Planarity : 0.003 0.040 714 Dihedral : 4.129 19.526 542 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.93 % Allowed : 8.16 % Favored : 90.91 % 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: 2.34 (0.38), residues: 499 helix: 1.91 (0.25), residues: 417 sheet: None (None), residues: 0 loop : -0.22 (0.71), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 169 HIS 0.003 0.001 HIS A 406 PHE 0.014 0.001 PHE A 338 TYR 0.010 0.001 TYR A 298 ARG 0.002 0.000 ARG A 529 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8185 (mm-30) REVERT: A 391 ASN cc_start: 0.7792 (m-40) cc_final: 0.7334 (p0) REVERT: A 450 TYR cc_start: 0.8275 (t80) cc_final: 0.7936 (t80) REVERT: A 462 MET cc_start: 0.7060 (mmt) cc_final: 0.6838 (mmt) outliers start: 4 outliers final: 2 residues processed: 70 average time/residue: 0.3697 time to fit residues: 32.1824 Evaluate side-chains 61 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain B residue 60 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 9 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3935 r_free = 0.3935 target = 0.150170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.124424 restraints weight = 16275.676| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.60 r_work: 0.3513 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4086 Z= 0.178 Angle : 0.472 4.221 5493 Z= 0.255 Chirality : 0.033 0.119 602 Planarity : 0.003 0.038 714 Dihedral : 4.028 18.294 542 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.17 % Allowed : 8.39 % Favored : 90.44 % 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: 2.50 (0.38), residues: 499 helix: 2.04 (0.25), residues: 417 sheet: None (None), residues: 0 loop : -0.29 (0.72), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 169 HIS 0.003 0.002 HIS A 515 PHE 0.013 0.001 PHE A 338 TYR 0.009 0.001 TYR A 186 ARG 0.003 0.000 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8218 (mm-30) REVERT: A 450 TYR cc_start: 0.8281 (t80) cc_final: 0.7950 (t80) outliers start: 5 outliers final: 3 residues processed: 64 average time/residue: 0.3171 time to fit residues: 26.7273 Evaluate side-chains 62 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain B residue 60 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 33 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3927 r_free = 0.3927 target = 0.149201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.123528 restraints weight = 16409.543| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.63 r_work: 0.3508 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.5293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4086 Z= 0.186 Angle : 0.468 4.257 5493 Z= 0.254 Chirality : 0.033 0.117 602 Planarity : 0.003 0.039 714 Dihedral : 3.956 17.981 542 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.93 % Allowed : 8.86 % Favored : 90.21 % 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: 2.58 (0.37), residues: 499 helix: 2.09 (0.25), residues: 418 sheet: None (None), residues: 0 loop : -0.28 (0.74), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 169 HIS 0.003 0.001 HIS A 406 PHE 0.014 0.001 PHE A 338 TYR 0.009 0.001 TYR A 298 ARG 0.002 0.000 ARG A 407 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8198 (mm-30) REVERT: A 246 ASN cc_start: 0.8795 (m-40) cc_final: 0.8559 (t0) REVERT: A 450 TYR cc_start: 0.8276 (t80) cc_final: 0.7930 (t80) outliers start: 4 outliers final: 4 residues processed: 64 average time/residue: 0.3900 time to fit residues: 31.3007 Evaluate side-chains 62 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain B residue 60 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 19 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3931 r_free = 0.3931 target = 0.149512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.123632 restraints weight = 16361.799| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.70 r_work: 0.3502 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.5376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4086 Z= 0.176 Angle : 0.465 4.510 5493 Z= 0.252 Chirality : 0.032 0.116 602 Planarity : 0.003 0.038 714 Dihedral : 3.904 17.537 542 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.40 % Allowed : 8.86 % Favored : 89.74 % 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 (0.37), residues: 499 helix: 2.18 (0.25), residues: 418 sheet: None (None), residues: 0 loop : -0.36 (0.73), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 169 HIS 0.003 0.001 HIS A 406 PHE 0.013 0.001 PHE A 338 TYR 0.008 0.001 TYR A 377 ARG 0.002 0.000 ARG A 407 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8164 (mm-30) REVERT: A 246 ASN cc_start: 0.8853 (m-40) cc_final: 0.8597 (t0) REVERT: A 450 TYR cc_start: 0.8294 (t80) cc_final: 0.7875 (t80) outliers start: 6 outliers final: 4 residues processed: 67 average time/residue: 0.3381 time to fit residues: 29.5045 Evaluate side-chains 63 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain B residue 60 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 14 optimal weight: 0.0050 chunk 16 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.147901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.122136 restraints weight = 16792.356| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.66 r_work: 0.3483 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.5510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4086 Z= 0.212 Angle : 0.487 4.304 5493 Z= 0.268 Chirality : 0.034 0.118 602 Planarity : 0.003 0.039 714 Dihedral : 4.005 17.411 542 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.40 % Allowed : 9.56 % Favored : 89.04 % 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: 2.56 (0.37), residues: 499 helix: 2.14 (0.24), residues: 413 sheet: None (None), residues: 0 loop : -0.48 (0.69), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 169 HIS 0.004 0.002 HIS A 515 PHE 0.014 0.001 PHE A 338 TYR 0.011 0.001 TYR A 377 ARG 0.003 0.000 ARG A 407 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8162 (mm-30) REVERT: A 167 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7731 (mp10) REVERT: A 450 TYR cc_start: 0.8244 (t80) cc_final: 0.7871 (t80) REVERT: A 551 MET cc_start: 0.8111 (ttp) cc_final: 0.7800 (tpp) REVERT: A 561 MET cc_start: 0.7795 (mmt) cc_final: 0.5856 (mmt) outliers start: 6 outliers final: 4 residues processed: 66 average time/residue: 0.3604 time to fit residues: 30.1575 Evaluate side-chains 62 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 GLN Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain B residue 60 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 18 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3920 r_free = 0.3920 target = 0.148148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.122362 restraints weight = 16798.278| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.72 r_work: 0.3491 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.5638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4086 Z= 0.191 Angle : 0.472 4.292 5493 Z= 0.258 Chirality : 0.033 0.113 602 Planarity : 0.003 0.038 714 Dihedral : 3.964 16.529 542 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.63 % Allowed : 10.02 % Favored : 88.34 % 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: 2.76 (0.37), residues: 499 helix: 2.27 (0.24), residues: 413 sheet: None (None), residues: 0 loop : -0.42 (0.69), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 169 HIS 0.003 0.001 HIS A 406 PHE 0.013 0.001 PHE A 338 TYR 0.010 0.001 TYR A 377 ARG 0.002 0.000 ARG A 407 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8157 (mm-30) REVERT: A 167 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7676 (mp10) REVERT: A 450 TYR cc_start: 0.8263 (t80) cc_final: 0.7872 (t80) REVERT: A 462 MET cc_start: 0.7456 (mmm) cc_final: 0.7195 (mmt) REVERT: A 551 MET cc_start: 0.7982 (ttp) cc_final: 0.7649 (tpp) REVERT: A 561 MET cc_start: 0.7708 (mmt) cc_final: 0.5800 (mmt) outliers start: 7 outliers final: 5 residues processed: 64 average time/residue: 0.3562 time to fit residues: 28.8230 Evaluate side-chains 61 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 GLN Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain B residue 60 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 14 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3938 r_free = 0.3938 target = 0.149660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.124073 restraints weight = 16366.463| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.69 r_work: 0.3524 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.5729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4086 Z= 0.154 Angle : 0.460 4.558 5493 Z= 0.248 Chirality : 0.032 0.114 602 Planarity : 0.003 0.039 714 Dihedral : 3.876 16.614 542 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.40 % Allowed : 10.72 % Favored : 87.88 % 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: 2.94 (0.37), residues: 499 helix: 2.42 (0.25), residues: 413 sheet: None (None), residues: 0 loop : -0.44 (0.68), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 169 HIS 0.003 0.001 HIS A 406 PHE 0.012 0.001 PHE A 338 TYR 0.008 0.001 TYR A 186 ARG 0.001 0.000 ARG A 529 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8183 (mm-30) REVERT: A 167 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7712 (mp10) REVERT: A 450 TYR cc_start: 0.8224 (t80) cc_final: 0.7808 (t80) REVERT: A 462 MET cc_start: 0.7460 (mmm) cc_final: 0.7209 (mmt) REVERT: A 561 MET cc_start: 0.7739 (mmt) cc_final: 0.5844 (mmt) outliers start: 6 outliers final: 5 residues processed: 60 average time/residue: 0.4023 time to fit residues: 31.0696 Evaluate side-chains 60 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 GLN Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain B residue 60 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 19 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 16 optimal weight: 0.0370 chunk 3 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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 = 0.3949 r_free = 0.3949 target = 0.150530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.125085 restraints weight = 16764.571| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.67 r_work: 0.3528 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.5804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4086 Z= 0.149 Angle : 0.453 4.653 5493 Z= 0.243 Chirality : 0.032 0.115 602 Planarity : 0.003 0.038 714 Dihedral : 3.780 15.708 542 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.17 % Allowed : 10.96 % Favored : 87.88 % 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: 3.04 (0.37), residues: 499 helix: 2.48 (0.25), residues: 415 sheet: None (None), residues: 0 loop : -0.45 (0.68), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 169 HIS 0.002 0.001 HIS A 406 PHE 0.011 0.001 PHE A 338 TYR 0.007 0.001 TYR A 186 ARG 0.001 0.000 ARG A 529 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5061.54 seconds wall clock time: 86 minutes 55.62 seconds (5215.62 seconds total)