Starting phenix.real_space_refine on Wed Feb 12 13:55:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kdt_22829/02_2025/7kdt_22829.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kdt_22829/02_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_22829/02_2025/7kdt_22829.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kdt_22829/02_2025/7kdt_22829.map" model { file = "/net/cci-nas-00/data/ceres_data/7kdt_22829/02_2025/7kdt_22829.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kdt_22829/02_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.20, per 1000 atoms: 0.52 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: 1.78 Conformation dependent library (CDL) restraints added in 619.3 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: 0.54 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: 2.56 Time building geometry restraints manager: 2.18 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: 1.280 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: 0.140 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.070 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.420 ------------------------------------------------------------------------------- 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 : 0.588 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: 0.4509 time to fit residues: 65.8820 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 : 0.608 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3963 r_free = 0.3963 target = 0.152127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.127559 restraints weight = 15791.253| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.52 r_work: 0.3564 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3675 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= 0.196 Angle : 0.601 5.417 5493 Z= 0.330 Chirality : 0.035 0.134 602 Planarity : 0.005 0.056 714 Dihedral : 4.959 23.815 542 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % 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 : -0.74 (0.61), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 169 HIS 0.004 0.002 HIS A 405 PHE 0.020 0.002 PHE A 338 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 85 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.674 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: A 238 GLU cc_start: 0.8247 (mt-10) cc_final: 0.8033 (tm-30) REVERT: A 392 MET cc_start: 0.7677 (mmp) cc_final: 0.7369 (tpt) REVERT: A 425 ASP cc_start: 0.8434 (t0) cc_final: 0.8140 (m-30) REVERT: A 462 MET cc_start: 0.7195 (mmt) cc_final: 0.6919 (mmt) REVERT: A 531 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7681 (tt) REVERT: B 59 LYS cc_start: 0.8173 (tttp) cc_final: 0.7965 (mtpt) outliers start: 4 outliers final: 2 residues processed: 82 average time/residue: 0.3525 time to fit residues: 36.2067 Evaluate side-chains 73 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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: 0.8980 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 14 optimal weight: 0.1980 chunk 41 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 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: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3954 r_free = 0.3954 target = 0.151917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.126000 restraints weight = 16255.690| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.75 r_work: 0.3543 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.4238 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= 0.172 Angle : 0.518 4.225 5493 Z= 0.281 Chirality : 0.033 0.119 602 Planarity : 0.004 0.047 714 Dihedral : 4.412 20.749 542 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.17 % Allowed : 6.99 % Favored : 91.84 % 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: 1.77 (0.37), residues: 499 helix: 1.53 (0.25), residues: 417 sheet: None (None), residues: 0 loop : -0.43 (0.68), 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 0.019 0.002 PHE A 163 TYR 0.014 0.001 TYR A 186 ARG 0.003 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 79 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 391 ASN cc_start: 0.7728 (m-40) cc_final: 0.7287 (p0) REVERT: A 425 ASP cc_start: 0.8302 (t0) cc_final: 0.7987 (m-30) REVERT: A 462 MET cc_start: 0.7071 (mmt) cc_final: 0.6773 (mmt) outliers start: 5 outliers final: 3 residues processed: 76 average time/residue: 0.3664 time to fit residues: 34.7607 Evaluate side-chains 65 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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: 2.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.151271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.125718 restraints weight = 16135.557| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.60 r_work: 0.3542 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4086 Z= 0.162 Angle : 0.485 5.205 5493 Z= 0.259 Chirality : 0.033 0.123 602 Planarity : 0.003 0.040 714 Dihedral : 4.155 19.469 542 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.85 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: 2.29 (0.38), residues: 499 helix: 1.87 (0.25), residues: 417 sheet: None (None), residues: 0 loop : -0.20 (0.71), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 169 HIS 0.003 0.001 HIS A 405 PHE 0.014 0.001 PHE A 338 TYR 0.010 0.001 TYR A 298 ARG 0.004 0.000 ARG A 159 *********************** 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 70 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8195 (mm-30) REVERT: A 450 TYR cc_start: 0.8294 (t80) cc_final: 0.7957 (t80) REVERT: A 462 MET cc_start: 0.7076 (mmt) cc_final: 0.6854 (mmt) outliers start: 5 outliers final: 3 residues processed: 69 average time/residue: 0.3503 time to fit residues: 30.4147 Evaluate side-chains 57 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 GLU 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: 0.9990 chunk 3 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.151148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.125320 restraints weight = 16143.811| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.67 r_work: 0.3530 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.5156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4086 Z= 0.150 Angle : 0.456 4.206 5493 Z= 0.245 Chirality : 0.032 0.116 602 Planarity : 0.003 0.039 714 Dihedral : 4.001 18.403 542 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % 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: 2.62 (0.38), residues: 499 helix: 2.11 (0.25), residues: 417 sheet: None (None), residues: 0 loop : -0.21 (0.71), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 169 HIS 0.003 0.001 HIS A 406 PHE 0.012 0.001 PHE A 338 TYR 0.009 0.001 TYR A 186 ARG 0.002 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 69 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.655 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 139 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8194 (mm-30) REVERT: A 450 TYR cc_start: 0.8303 (t80) cc_final: 0.7938 (t80) outliers start: 6 outliers final: 3 residues processed: 66 average time/residue: 0.2928 time to fit residues: 25.2287 Evaluate side-chains 63 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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: 0.7980 chunk 44 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 3 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 0.0470 overall best weight: 0.8480 ------------------------------------------------------------------------------- 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 = 0.3943 r_free = 0.3943 target = 0.150531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.125050 restraints weight = 16287.820| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.61 r_work: 0.3529 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.5300 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= 0.159 Angle : 0.458 4.191 5493 Z= 0.245 Chirality : 0.032 0.115 602 Planarity : 0.003 0.039 714 Dihedral : 3.895 17.690 542 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.93 % Allowed : 9.32 % 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: 2.77 (0.38), residues: 499 helix: 2.22 (0.25), residues: 417 sheet: None (None), residues: 0 loop : -0.14 (0.72), residues: 82 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 0.012 0.001 PHE A 338 TYR 0.008 0.001 TYR A 298 ARG 0.002 0.000 ARG A 159 *********************** 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 63 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.652 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: A 139 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8189 (mm-30) REVERT: A 246 ASN cc_start: 0.8789 (m-40) cc_final: 0.8563 (t0) REVERT: A 247 ARG cc_start: 0.7708 (ttp80) cc_final: 0.7029 (ptm-80) REVERT: A 450 TYR cc_start: 0.8300 (t80) cc_final: 0.7932 (t80) outliers start: 4 outliers final: 4 residues processed: 62 average time/residue: 0.3435 time to fit residues: 27.4104 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 : 0.715 ------------------------------------------------------------------------------- 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: 5.9990 chunk 33 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3934 r_free = 0.3934 target = 0.149787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.124188 restraints weight = 16268.243| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.62 r_work: 0.3515 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.5305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4086 Z= 0.171 Angle : 0.460 4.440 5493 Z= 0.248 Chirality : 0.032 0.117 602 Planarity : 0.003 0.039 714 Dihedral : 3.866 17.210 542 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.93 % Allowed : 9.56 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.82 (0.37), residues: 499 helix: 2.27 (0.25), residues: 417 sheet: None (None), residues: 0 loop : -0.23 (0.72), residues: 82 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 159 *********************** 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 66 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.655 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 139 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8182 (mm-30) REVERT: A 246 ASN cc_start: 0.8790 (m-40) cc_final: 0.8581 (t0) REVERT: A 450 TYR cc_start: 0.8325 (t80) cc_final: 0.7978 (t80) REVERT: A 561 MET cc_start: 0.7918 (mmt) cc_final: 0.6132 (mmt) outliers start: 4 outliers final: 4 residues processed: 65 average time/residue: 0.3574 time to fit residues: 29.0755 Evaluate side-chains 61 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.857 ------------------------------------------------------------------------------- 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: 2.9990 chunk 6 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.3915 r_free = 0.3915 target = 0.147766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.121701 restraints weight = 16683.708| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.72 r_work: 0.3478 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.5395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4086 Z= 0.227 Angle : 0.488 4.281 5493 Z= 0.267 Chirality : 0.034 0.120 602 Planarity : 0.003 0.038 714 Dihedral : 3.988 16.780 542 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.17 % Allowed : 9.79 % 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: 2.59 (0.37), residues: 499 helix: 2.14 (0.24), residues: 416 sheet: None (None), residues: 0 loop : -0.47 (0.70), residues: 83 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 0.012 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 65 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8130 (mm-30) REVERT: A 158 ASN cc_start: 0.8547 (m-40) cc_final: 0.8241 (m-40) REVERT: A 271 GLN cc_start: 0.7286 (mt0) cc_final: 0.7040 (mt0) REVERT: A 551 MET cc_start: 0.8061 (ttp) cc_final: 0.7709 (tpp) REVERT: A 561 MET cc_start: 0.7731 (mmt) cc_final: 0.5805 (mmt) outliers start: 5 outliers final: 4 residues processed: 64 average time/residue: 0.3752 time to fit residues: 29.6559 Evaluate side-chains 61 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 18 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3941 r_free = 0.3941 target = 0.150595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.124759 restraints weight = 16725.784| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.67 r_work: 0.3513 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.5551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4086 Z= 0.157 Angle : 0.457 4.285 5493 Z= 0.245 Chirality : 0.032 0.112 602 Planarity : 0.003 0.038 714 Dihedral : 3.857 16.688 542 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.70 % Allowed : 10.26 % 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: 2.94 (0.37), residues: 499 helix: 2.41 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -0.39 (0.69), residues: 87 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 0.012 0.001 PHE A 338 TYR 0.007 0.001 TYR A 377 ARG 0.001 0.000 ARG A 159 *********************** 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 62 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8178 (mm-30) REVERT: A 268 ILE cc_start: 0.7758 (mp) cc_final: 0.7489 (mp) REVERT: A 450 TYR cc_start: 0.8298 (t80) cc_final: 0.7874 (t80) REVERT: A 462 MET cc_start: 0.7555 (mmm) cc_final: 0.7306 (mmt) REVERT: A 551 MET cc_start: 0.8117 (ttp) cc_final: 0.7789 (tpp) REVERT: A 561 MET cc_start: 0.7870 (mmt) cc_final: 0.6040 (mmt) outliers start: 3 outliers final: 3 residues processed: 61 average time/residue: 0.3708 time to fit residues: 28.5221 Evaluate side-chains 59 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 10 optimal weight: 0.0470 chunk 19 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 14 optimal weight: 0.0870 overall best weight: 0.9258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.149448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.123790 restraints weight = 16326.945| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.67 r_work: 0.3507 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.5589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4086 Z= 0.168 Angle : 0.460 4.263 5493 Z= 0.248 Chirality : 0.032 0.113 602 Planarity : 0.003 0.038 714 Dihedral : 3.868 17.265 542 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.70 % Allowed : 10.49 % Favored : 88.81 % 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: 2.98 (0.37), residues: 499 helix: 2.43 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -0.33 (0.68), residues: 87 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 0.012 0.001 PHE A 338 TYR 0.008 0.001 TYR A 377 ARG 0.002 0.000 ARG A 407 ********************** 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 60 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8177 (mm-30) REVERT: A 450 TYR cc_start: 0.8308 (t80) cc_final: 0.7901 (t80) REVERT: A 462 MET cc_start: 0.7574 (mmm) cc_final: 0.7296 (mmt) REVERT: A 561 MET cc_start: 0.7805 (mmt) cc_final: 0.5995 (mmt) outliers start: 3 outliers final: 3 residues processed: 59 average time/residue: 0.3382 time to fit residues: 25.3833 Evaluate side-chains 58 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 19 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 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: 1.9990 chunk 44 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.149130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.123401 restraints weight = 16718.040| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.70 r_work: 0.3504 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.5643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4086 Z= 0.176 Angle : 0.467 4.243 5493 Z= 0.252 Chirality : 0.033 0.115 602 Planarity : 0.003 0.038 714 Dihedral : 3.900 16.311 542 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.70 % Allowed : 10.26 % 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: 2.96 (0.37), residues: 499 helix: 2.43 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -0.40 (0.67), residues: 87 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 0.009 0.001 TYR A 377 ARG 0.002 0.000 ARG A 407 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4730.35 seconds wall clock time: 83 minutes 43.43 seconds (5023.43 seconds total)