Starting phenix.real_space_refine on Thu Jul 24 05:29:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n93_49158/07_2025/9n93_49158.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n93_49158/07_2025/9n93_49158.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n93_49158/07_2025/9n93_49158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n93_49158/07_2025/9n93_49158.map" model { file = "/net/cci-nas-00/data/ceres_data/9n93_49158/07_2025/9n93_49158.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n93_49158/07_2025/9n93_49158.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 3493 2.51 5 N 848 2.21 5 O 896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 5275 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5275 Classifications: {'peptide': 650} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 26, 'TRANS': 623} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 4.14, per 1000 atoms: 0.78 Number of scatterers: 5275 At special positions: 0 Unit cell: (86.87, 81.76, 92.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 38 16.00 O 896 8.00 N 848 7.00 C 3493 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 649.7 milliseconds 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1244 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 2 sheets defined 70.5% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 49 through 72 Processing helix chain 'A' and resid 77 through 81 removed outlier: 3.500A pdb=" N ILE A 81 " --> pdb=" O TYR A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 132 through 160 removed outlier: 4.194A pdb=" N ALA A 136 " --> pdb=" O CYS A 132 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 137 " --> pdb=" O GLY A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 167 Processing helix chain 'A' and resid 178 through 186 removed outlier: 6.236A pdb=" N ILE A 183 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ALA A 184 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 221 removed outlier: 3.787A pdb=" N HIS A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 251 Processing helix chain 'A' and resid 267 through 294 removed outlier: 3.592A pdb=" N GLN A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 343 removed outlier: 4.266A pdb=" N GLN A 343 " --> pdb=" O GLU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 369 Processing helix chain 'A' and resid 391 through 395 Processing helix chain 'A' and resid 402 through 406 removed outlier: 3.897A pdb=" N ILE A 406 " --> pdb=" O PRO A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 411 Processing helix chain 'A' and resid 418 through 437 removed outlier: 4.004A pdb=" N PHE A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR A 428 " --> pdb=" O GLY A 424 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 449 Processing helix chain 'A' and resid 461 through 466 Processing helix chain 'A' and resid 466 through 489 Proline residue: A 480 - end of helix removed outlier: 4.049A pdb=" N THR A 487 " --> pdb=" O VAL A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 514 removed outlier: 3.555A pdb=" N PHE A 512 " --> pdb=" O ILE A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 521 Processing helix chain 'A' and resid 524 through 533 Processing helix chain 'A' and resid 542 through 546 Processing helix chain 'A' and resid 551 through 574 removed outlier: 3.772A pdb=" N GLY A 567 " --> pdb=" O SER A 563 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASN A 568 " --> pdb=" O ALA A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 587 Processing helix chain 'A' and resid 592 through 602 removed outlier: 3.531A pdb=" N VAL A 597 " --> pdb=" O ASP A 593 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ALA A 602 " --> pdb=" O LYS A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 624 removed outlier: 3.686A pdb=" N TRP A 613 " --> pdb=" O ALA A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 653 removed outlier: 4.224A pdb=" N PHE A 634 " --> pdb=" O ILE A 630 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR A 651 " --> pdb=" O ARG A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 672 removed outlier: 3.848A pdb=" N LEU A 672 " --> pdb=" O VAL A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 690 Processing helix chain 'A' and resid 694 through 719 Processing sheet with id=AA1, first strand: chain 'A' and resid 257 through 264 removed outlier: 5.159A pdb=" N VAL A 257 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N THR A 353 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ASP A 259 " --> pdb=" O PHE A 351 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N PHE A 351 " --> pdb=" O ASP A 259 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLN A 261 " --> pdb=" O MET A 349 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N MET A 349 " --> pdb=" O GLN A 261 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N CYS A 263 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 298 through 299 326 hydrogen bonds defined for protein. 936 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: 1.48 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1030 1.33 - 1.45: 1367 1.45 - 1.57: 2973 1.57 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 5424 Sorted by residual: bond pdb=" C SER A 476 " pdb=" O SER A 476 " ideal model delta sigma weight residual 1.236 1.319 -0.083 1.16e-02 7.43e+03 5.08e+01 bond pdb=" C TRP A 473 " pdb=" O TRP A 473 " ideal model delta sigma weight residual 1.236 1.296 -0.059 1.15e-02 7.56e+03 2.67e+01 bond pdb=" C LEU A 479 " pdb=" O LEU A 479 " ideal model delta sigma weight residual 1.244 1.284 -0.040 9.40e-03 1.13e+04 1.83e+01 bond pdb=" N ASP A 405 " pdb=" CA ASP A 405 " ideal model delta sigma weight residual 1.456 1.497 -0.040 1.22e-02 6.72e+03 1.08e+01 bond pdb=" N ILE A 462 " pdb=" CA ILE A 462 " ideal model delta sigma weight residual 1.462 1.496 -0.034 1.18e-02 7.18e+03 8.32e+00 ... (remaining 5419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 7190 1.88 - 3.77: 146 3.77 - 5.65: 30 5.65 - 7.53: 7 7.53 - 9.41: 2 Bond angle restraints: 7375 Sorted by residual: angle pdb=" C SER A 486 " pdb=" N THR A 487 " pdb=" CA THR A 487 " ideal model delta sigma weight residual 122.42 131.83 -9.41 1.77e+00 3.19e-01 2.83e+01 angle pdb=" CA PRO A 480 " pdb=" N PRO A 480 " pdb=" CD PRO A 480 " ideal model delta sigma weight residual 112.00 105.12 6.88 1.40e+00 5.10e-01 2.41e+01 angle pdb=" C ILE A 482 " pdb=" N VAL A 483 " pdb=" CA VAL A 483 " ideal model delta sigma weight residual 120.46 113.74 6.72 1.37e+00 5.33e-01 2.40e+01 angle pdb=" N GLU A 545 " pdb=" CA GLU A 545 " pdb=" C GLU A 545 " ideal model delta sigma weight residual 114.56 108.79 5.77 1.27e+00 6.20e-01 2.06e+01 angle pdb=" CA ASP A 405 " pdb=" CB ASP A 405 " pdb=" CG ASP A 405 " ideal model delta sigma weight residual 112.60 117.13 -4.53 1.00e+00 1.00e+00 2.05e+01 ... (remaining 7370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 2877 17.75 - 35.50: 221 35.50 - 53.24: 47 53.24 - 70.99: 10 70.99 - 88.74: 3 Dihedral angle restraints: 3158 sinusoidal: 1240 harmonic: 1918 Sorted by residual: dihedral pdb=" CA LEU A 488 " pdb=" C LEU A 488 " pdb=" N LEU A 489 " pdb=" CA LEU A 489 " ideal model delta harmonic sigma weight residual 180.00 159.13 20.87 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA VAL A 653 " pdb=" C VAL A 653 " pdb=" N TYR A 654 " pdb=" CA TYR A 654 " ideal model delta harmonic sigma weight residual 180.00 159.80 20.20 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA THR A 487 " pdb=" C THR A 487 " pdb=" N LEU A 488 " pdb=" CA LEU A 488 " ideal model delta harmonic sigma weight residual 180.00 160.53 19.47 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 3155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 630 0.045 - 0.091: 169 0.091 - 0.136: 35 0.136 - 0.181: 8 0.181 - 0.226: 1 Chirality restraints: 843 Sorted by residual: chirality pdb=" CA ILE A 482 " pdb=" N ILE A 482 " pdb=" C ILE A 482 " pdb=" CB ILE A 482 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CG LEU A 479 " pdb=" CB LEU A 479 " pdb=" CD1 LEU A 479 " pdb=" CD2 LEU A 479 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 7.87e-01 chirality pdb=" CB VAL A 483 " pdb=" CA VAL A 483 " pdb=" CG1 VAL A 483 " pdb=" CG2 VAL A 483 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.64e-01 ... (remaining 840 not shown) Planarity restraints: 902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 479 " -0.075 5.00e-02 4.00e+02 1.11e-01 1.97e+01 pdb=" N PRO A 480 " 0.192 5.00e-02 4.00e+02 pdb=" CA PRO A 480 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 480 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 418 " 0.020 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C TRP A 418 " -0.068 2.00e-02 2.50e+03 pdb=" O TRP A 418 " 0.025 2.00e-02 2.50e+03 pdb=" N TRP A 419 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 368 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.67e+00 pdb=" C ASN A 368 " -0.045 2.00e-02 2.50e+03 pdb=" O ASN A 368 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA A 369 " 0.015 2.00e-02 2.50e+03 ... (remaining 899 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 876 2.76 - 3.29: 5218 3.29 - 3.83: 8864 3.83 - 4.36: 10363 4.36 - 4.90: 17977 Nonbonded interactions: 43298 Sorted by model distance: nonbonded pdb=" OG1 THR A 438 " pdb=" O THR A 523 " model vdw 2.222 3.040 nonbonded pdb=" ND2 ASN A 368 " pdb=" O VAL A 397 " model vdw 2.268 3.120 nonbonded pdb=" OD1 ASP A 169 " pdb=" NE2 GLN A 187 " model vdw 2.309 3.120 nonbonded pdb=" O ASN A 596 " pdb=" ND2 ASN A 600 " model vdw 2.318 3.120 nonbonded pdb=" O LEU A 433 " pdb=" OG1 THR A 437 " model vdw 2.325 3.040 ... (remaining 43293 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 17.850 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:12.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 5424 Z= 0.287 Angle : 0.670 9.414 7375 Z= 0.413 Chirality : 0.043 0.226 843 Planarity : 0.006 0.111 902 Dihedral : 13.479 88.738 1914 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 0.35 % Allowed : 10.05 % Favored : 89.60 % 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: 0.24 (0.35), residues: 644 helix: 0.89 (0.26), residues: 435 sheet: -1.81 (1.65), residues: 12 loop : -1.29 (0.50), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 473 HIS 0.002 0.001 HIS A 643 PHE 0.012 0.001 PHE A 618 TYR 0.018 0.002 TYR A 484 ARG 0.002 0.000 ARG A 80 Details of bonding type rmsd hydrogen bonds : bond 0.12653 ( 326) hydrogen bonds : angle 5.73822 ( 936) covalent geometry : bond 0.00442 ( 5424) covalent geometry : angle 0.67037 ( 7375) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.572 Fit side-chains REVERT: A 159 CYS cc_start: 0.8336 (m) cc_final: 0.7626 (t) REVERT: A 212 ARG cc_start: 0.6806 (mpt180) cc_final: 0.6520 (ttp80) REVERT: A 216 GLN cc_start: 0.8196 (mm-40) cc_final: 0.7886 (mt0) REVERT: A 318 GLU cc_start: 0.6692 (tm-30) cc_final: 0.6236 (tm-30) REVERT: A 394 LYS cc_start: 0.8196 (mptt) cc_final: 0.7924 (mmtp) REVERT: A 404 GLU cc_start: 0.7576 (mm-30) cc_final: 0.6951 (mm-30) REVERT: A 587 MET cc_start: 0.7456 (mtt) cc_final: 0.7217 (mtp) REVERT: A 606 GLU cc_start: 0.7485 (pt0) cc_final: 0.7190 (mt-10) outliers start: 2 outliers final: 1 residues processed: 86 average time/residue: 1.0204 time to fit residues: 92.3824 Evaluate side-chains 69 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 16 optimal weight: 0.0040 chunk 33 optimal weight: 0.0050 chunk 26 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 8.9990 chunk 37 optimal weight: 0.3980 chunk 59 optimal weight: 0.9980 overall best weight: 0.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.154586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.119171 restraints weight = 5897.138| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.97 r_work: 0.3298 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5424 Z= 0.113 Angle : 0.512 6.538 7375 Z= 0.270 Chirality : 0.040 0.184 843 Planarity : 0.004 0.038 902 Dihedral : 4.214 20.530 705 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.08 % Allowed : 13.34 % Favored : 84.58 % 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: 0.58 (0.35), residues: 644 helix: 1.26 (0.25), residues: 437 sheet: -1.99 (1.23), residues: 17 loop : -1.42 (0.50), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 408 HIS 0.002 0.001 HIS A 714 PHE 0.010 0.001 PHE A 618 TYR 0.017 0.002 TYR A 252 ARG 0.001 0.000 ARG A 80 Details of bonding type rmsd hydrogen bonds : bond 0.03751 ( 326) hydrogen bonds : angle 4.49920 ( 936) covalent geometry : bond 0.00236 ( 5424) covalent geometry : angle 0.51222 ( 7375) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.620 Fit side-chains REVERT: A 159 CYS cc_start: 0.8336 (m) cc_final: 0.7538 (t) REVERT: A 212 ARG cc_start: 0.6793 (mpt180) cc_final: 0.6432 (ttp80) REVERT: A 216 GLN cc_start: 0.7949 (mm-40) cc_final: 0.7737 (mt0) REVERT: A 318 GLU cc_start: 0.6572 (tm-30) cc_final: 0.6350 (tm-30) REVERT: A 394 LYS cc_start: 0.8240 (mptt) cc_final: 0.7993 (mptp) REVERT: A 404 GLU cc_start: 0.7544 (mm-30) cc_final: 0.6881 (mm-30) REVERT: A 587 MET cc_start: 0.7346 (mtt) cc_final: 0.7070 (mtp) REVERT: A 593 ASP cc_start: 0.8055 (m-30) cc_final: 0.7692 (m-30) REVERT: A 606 GLU cc_start: 0.7640 (pt0) cc_final: 0.7258 (mt-10) outliers start: 12 outliers final: 6 residues processed: 86 average time/residue: 1.0599 time to fit residues: 96.7014 Evaluate side-chains 76 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 698 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 46 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 59 optimal weight: 0.4980 chunk 60 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.152309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.116400 restraints weight = 5959.999| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.97 r_work: 0.3260 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5424 Z= 0.134 Angle : 0.523 7.362 7375 Z= 0.271 Chirality : 0.040 0.171 843 Planarity : 0.004 0.037 902 Dihedral : 4.166 20.238 702 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.12 % Allowed : 15.08 % Favored : 81.80 % 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: 0.64 (0.35), residues: 644 helix: 1.33 (0.25), residues: 438 sheet: -1.90 (1.20), residues: 17 loop : -1.48 (0.50), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 418 HIS 0.002 0.001 HIS A 213 PHE 0.010 0.001 PHE A 618 TYR 0.025 0.002 TYR A 252 ARG 0.002 0.000 ARG A 80 Details of bonding type rmsd hydrogen bonds : bond 0.03829 ( 326) hydrogen bonds : angle 4.44790 ( 936) covalent geometry : bond 0.00302 ( 5424) covalent geometry : angle 0.52288 ( 7375) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.632 Fit side-chains REVERT: A 159 CYS cc_start: 0.8322 (m) cc_final: 0.7544 (t) REVERT: A 212 ARG cc_start: 0.6854 (mpt180) cc_final: 0.6497 (ttp80) REVERT: A 318 GLU cc_start: 0.6523 (tm-30) cc_final: 0.6071 (pt0) REVERT: A 394 LYS cc_start: 0.8257 (mptt) cc_final: 0.8006 (mptp) REVERT: A 404 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7043 (mm-30) REVERT: A 570 MET cc_start: 0.7962 (mmm) cc_final: 0.7583 (mmm) REVERT: A 587 MET cc_start: 0.7370 (mtt) cc_final: 0.7082 (mtp) REVERT: A 593 ASP cc_start: 0.8007 (m-30) cc_final: 0.7623 (m-30) REVERT: A 606 GLU cc_start: 0.7769 (pt0) cc_final: 0.7344 (mt-10) REVERT: A 706 LEU cc_start: 0.7397 (mt) cc_final: 0.6605 (tp) outliers start: 18 outliers final: 8 residues processed: 86 average time/residue: 0.9795 time to fit residues: 88.9599 Evaluate side-chains 77 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 690 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 45 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 0.0270 chunk 37 optimal weight: 0.0980 chunk 16 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.154230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.118669 restraints weight = 6095.089| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.93 r_work: 0.3283 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5424 Z= 0.111 Angle : 0.500 6.720 7375 Z= 0.257 Chirality : 0.040 0.161 843 Planarity : 0.004 0.035 902 Dihedral : 4.036 19.400 702 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.12 % Allowed : 15.60 % Favored : 81.28 % 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: 0.77 (0.35), residues: 644 helix: 1.44 (0.25), residues: 438 sheet: -2.02 (1.20), residues: 17 loop : -1.44 (0.48), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 418 HIS 0.002 0.000 HIS A 214 PHE 0.009 0.001 PHE A 142 TYR 0.020 0.002 TYR A 252 ARG 0.001 0.000 ARG A 80 Details of bonding type rmsd hydrogen bonds : bond 0.03566 ( 326) hydrogen bonds : angle 4.33881 ( 936) covalent geometry : bond 0.00240 ( 5424) covalent geometry : angle 0.49958 ( 7375) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.570 Fit side-chains REVERT: A 53 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.7350 (mmm) REVERT: A 159 CYS cc_start: 0.8267 (m) cc_final: 0.7501 (t) REVERT: A 212 ARG cc_start: 0.6919 (mpt180) cc_final: 0.6558 (ttp80) REVERT: A 280 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7614 (mm-30) REVERT: A 318 GLU cc_start: 0.6582 (tm-30) cc_final: 0.6116 (pt0) REVERT: A 394 LYS cc_start: 0.8256 (mptt) cc_final: 0.8015 (mptp) REVERT: A 404 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7175 (mt-10) REVERT: A 463 ILE cc_start: 0.6781 (OUTLIER) cc_final: 0.6452 (pt) REVERT: A 570 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7697 (mmm) REVERT: A 587 MET cc_start: 0.7331 (mtt) cc_final: 0.7045 (mtt) REVERT: A 593 ASP cc_start: 0.8064 (m-30) cc_final: 0.7650 (m-30) outliers start: 18 outliers final: 7 residues processed: 81 average time/residue: 0.9564 time to fit residues: 81.8999 Evaluate side-chains 78 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 702 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 62 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 30 optimal weight: 0.0000 chunk 25 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 18 optimal weight: 0.4980 chunk 14 optimal weight: 0.5980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.153249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.117832 restraints weight = 6060.533| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.92 r_work: 0.3283 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5424 Z= 0.120 Angle : 0.508 7.068 7375 Z= 0.261 Chirality : 0.040 0.158 843 Planarity : 0.004 0.034 902 Dihedral : 4.012 19.291 702 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.99 % Allowed : 16.29 % Favored : 79.72 % 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: 0.78 (0.35), residues: 644 helix: 1.44 (0.25), residues: 439 sheet: -1.93 (1.20), residues: 17 loop : -1.44 (0.49), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 418 HIS 0.002 0.000 HIS A 214 PHE 0.008 0.001 PHE A 618 TYR 0.021 0.001 TYR A 252 ARG 0.001 0.000 ARG A 228 Details of bonding type rmsd hydrogen bonds : bond 0.03638 ( 326) hydrogen bonds : angle 4.32684 ( 936) covalent geometry : bond 0.00267 ( 5424) covalent geometry : angle 0.50825 ( 7375) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.626 Fit side-chains REVERT: A 53 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7383 (mmm) REVERT: A 159 CYS cc_start: 0.8252 (m) cc_final: 0.7520 (t) REVERT: A 212 ARG cc_start: 0.6897 (mpt180) cc_final: 0.6528 (ttp80) REVERT: A 228 ARG cc_start: 0.7765 (mtm180) cc_final: 0.7558 (mtm180) REVERT: A 318 GLU cc_start: 0.6563 (tm-30) cc_final: 0.6147 (pt0) REVERT: A 394 LYS cc_start: 0.8260 (mptt) cc_final: 0.8032 (mptp) REVERT: A 404 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7151 (mt-10) REVERT: A 463 ILE cc_start: 0.6767 (OUTLIER) cc_final: 0.6417 (pt) REVERT: A 484 TYR cc_start: 0.8644 (t80) cc_final: 0.8238 (t80) REVERT: A 570 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7697 (mmm) REVERT: A 587 MET cc_start: 0.7288 (mtt) cc_final: 0.6986 (mtt) REVERT: A 606 GLU cc_start: 0.7836 (pt0) cc_final: 0.7478 (mt-10) REVERT: A 706 LEU cc_start: 0.7414 (mt) cc_final: 0.6651 (tp) outliers start: 23 outliers final: 8 residues processed: 81 average time/residue: 1.0101 time to fit residues: 86.4469 Evaluate side-chains 79 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 702 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 28 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 18 optimal weight: 0.0770 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 HIS A 414 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.151111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.115154 restraints weight = 5998.348| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.99 r_work: 0.3239 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5424 Z= 0.137 Angle : 0.521 7.763 7375 Z= 0.268 Chirality : 0.041 0.161 843 Planarity : 0.004 0.034 902 Dihedral : 4.068 19.409 702 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.16 % Allowed : 16.81 % Favored : 79.03 % 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: 0.72 (0.35), residues: 644 helix: 1.38 (0.25), residues: 439 sheet: -1.99 (1.19), residues: 17 loop : -1.43 (0.49), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 418 HIS 0.002 0.001 HIS A 214 PHE 0.014 0.001 PHE A 155 TYR 0.023 0.002 TYR A 252 ARG 0.001 0.000 ARG A 80 Details of bonding type rmsd hydrogen bonds : bond 0.03750 ( 326) hydrogen bonds : angle 4.37004 ( 936) covalent geometry : bond 0.00315 ( 5424) covalent geometry : angle 0.52146 ( 7375) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.577 Fit side-chains REVERT: A 53 MET cc_start: 0.7701 (OUTLIER) cc_final: 0.7277 (mmm) REVERT: A 159 CYS cc_start: 0.8306 (m) cc_final: 0.7508 (t) REVERT: A 212 ARG cc_start: 0.6846 (mpt180) cc_final: 0.6458 (ttp80) REVERT: A 318 GLU cc_start: 0.6467 (tm-30) cc_final: 0.5939 (pt0) REVERT: A 347 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7973 (mp) REVERT: A 394 LYS cc_start: 0.8262 (mptt) cc_final: 0.8024 (mptp) REVERT: A 404 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7209 (mt-10) REVERT: A 463 ILE cc_start: 0.6706 (OUTLIER) cc_final: 0.6311 (pt) REVERT: A 484 TYR cc_start: 0.8582 (t80) cc_final: 0.8207 (t80) REVERT: A 570 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7572 (mmm) REVERT: A 587 MET cc_start: 0.7326 (mtt) cc_final: 0.7007 (mtt) REVERT: A 606 GLU cc_start: 0.7825 (pt0) cc_final: 0.7399 (mt-10) REVERT: A 706 LEU cc_start: 0.7407 (mt) cc_final: 0.6632 (tp) outliers start: 24 outliers final: 10 residues processed: 85 average time/residue: 0.8703 time to fit residues: 78.6117 Evaluate side-chains 81 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 702 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 23 optimal weight: 8.9990 chunk 8 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.150256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.114288 restraints weight = 5933.426| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.98 r_work: 0.3224 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5424 Z= 0.148 Angle : 0.534 8.080 7375 Z= 0.274 Chirality : 0.041 0.161 843 Planarity : 0.004 0.034 902 Dihedral : 4.117 19.527 702 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 4.51 % Allowed : 17.50 % Favored : 77.99 % 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: 0.67 (0.35), residues: 644 helix: 1.35 (0.25), residues: 439 sheet: -1.98 (1.20), residues: 17 loop : -1.47 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 418 HIS 0.002 0.001 HIS A 214 PHE 0.009 0.001 PHE A 548 TYR 0.020 0.002 TYR A 252 ARG 0.002 0.000 ARG A 228 Details of bonding type rmsd hydrogen bonds : bond 0.03833 ( 326) hydrogen bonds : angle 4.39869 ( 936) covalent geometry : bond 0.00344 ( 5424) covalent geometry : angle 0.53409 ( 7375) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.666 Fit side-chains REVERT: A 53 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7340 (mmm) REVERT: A 159 CYS cc_start: 0.8345 (m) cc_final: 0.7578 (t) REVERT: A 212 ARG cc_start: 0.6893 (mpt180) cc_final: 0.6498 (ttp80) REVERT: A 302 LYS cc_start: 0.6364 (mmtm) cc_final: 0.6107 (mmtm) REVERT: A 318 GLU cc_start: 0.6417 (tm-30) cc_final: 0.5831 (pt0) REVERT: A 347 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7963 (mp) REVERT: A 394 LYS cc_start: 0.8276 (mptt) cc_final: 0.8038 (mptp) REVERT: A 404 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7255 (mt-10) REVERT: A 570 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7766 (mmm) REVERT: A 587 MET cc_start: 0.7357 (mtt) cc_final: 0.7062 (mtt) REVERT: A 706 LEU cc_start: 0.7443 (mt) cc_final: 0.6661 (tp) outliers start: 26 outliers final: 11 residues processed: 87 average time/residue: 0.9258 time to fit residues: 85.3678 Evaluate side-chains 84 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 702 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 0.7980 chunk 64 optimal weight: 0.0970 chunk 25 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 chunk 9 optimal weight: 0.2980 chunk 47 optimal weight: 0.0070 chunk 6 optimal weight: 0.2980 chunk 58 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 41 optimal weight: 0.4980 overall best weight: 0.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.155243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.119817 restraints weight = 5971.505| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.01 r_work: 0.3308 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5424 Z= 0.099 Angle : 0.491 6.736 7375 Z= 0.252 Chirality : 0.039 0.150 843 Planarity : 0.004 0.032 902 Dihedral : 3.893 17.966 702 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.95 % Allowed : 19.58 % Favored : 77.47 % 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: 0.91 (0.35), residues: 644 helix: 1.58 (0.25), residues: 438 sheet: -1.95 (1.22), residues: 17 loop : -1.50 (0.48), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 418 HIS 0.003 0.000 HIS A 214 PHE 0.010 0.001 PHE A 720 TYR 0.016 0.001 TYR A 285 ARG 0.001 0.000 ARG A 330 Details of bonding type rmsd hydrogen bonds : bond 0.03384 ( 326) hydrogen bonds : angle 4.19336 ( 936) covalent geometry : bond 0.00195 ( 5424) covalent geometry : angle 0.49091 ( 7375) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.638 Fit side-chains REVERT: A 53 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.7235 (mmm) REVERT: A 127 GLN cc_start: 0.8077 (mt0) cc_final: 0.7642 (mt0) REVERT: A 159 CYS cc_start: 0.8269 (m) cc_final: 0.7454 (t) REVERT: A 212 ARG cc_start: 0.6665 (mpt180) cc_final: 0.6328 (ttp80) REVERT: A 250 ASP cc_start: 0.7656 (t0) cc_final: 0.7438 (t0) REVERT: A 318 GLU cc_start: 0.6330 (tm-30) cc_final: 0.5805 (pt0) REVERT: A 347 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7886 (mp) REVERT: A 394 LYS cc_start: 0.8285 (mptt) cc_final: 0.8049 (mptp) REVERT: A 402 ASP cc_start: 0.7853 (t70) cc_final: 0.7355 (t70) REVERT: A 404 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7269 (mt-10) REVERT: A 587 MET cc_start: 0.7254 (mtt) cc_final: 0.6922 (mtt) REVERT: A 604 GLN cc_start: 0.8290 (mt0) cc_final: 0.7598 (mp10) outliers start: 17 outliers final: 7 residues processed: 86 average time/residue: 0.9334 time to fit residues: 85.2289 Evaluate side-chains 77 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 682 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 41 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 58 optimal weight: 0.0970 chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.152060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.116240 restraints weight = 5956.469| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.99 r_work: 0.3252 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5424 Z= 0.127 Angle : 0.524 9.642 7375 Z= 0.267 Chirality : 0.040 0.160 843 Planarity : 0.004 0.033 902 Dihedral : 3.963 19.208 702 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.08 % Allowed : 20.80 % Favored : 77.12 % 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: 0.91 (0.35), residues: 644 helix: 1.58 (0.25), residues: 437 sheet: -2.02 (1.22), residues: 17 loop : -1.47 (0.48), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 418 HIS 0.002 0.000 HIS A 214 PHE 0.020 0.001 PHE A 155 TYR 0.016 0.001 TYR A 484 ARG 0.001 0.000 ARG A 417 Details of bonding type rmsd hydrogen bonds : bond 0.03610 ( 326) hydrogen bonds : angle 4.27633 ( 936) covalent geometry : bond 0.00288 ( 5424) covalent geometry : angle 0.52382 ( 7375) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.612 Fit side-chains REVERT: A 53 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7258 (mmm) REVERT: A 127 GLN cc_start: 0.8114 (mt0) cc_final: 0.7836 (mt0) REVERT: A 159 CYS cc_start: 0.8247 (m) cc_final: 0.7453 (t) REVERT: A 212 ARG cc_start: 0.6708 (mpt180) cc_final: 0.6347 (ttp80) REVERT: A 250 ASP cc_start: 0.7709 (t0) cc_final: 0.7492 (t0) REVERT: A 318 GLU cc_start: 0.6265 (tm-30) cc_final: 0.5723 (pt0) REVERT: A 347 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7942 (mp) REVERT: A 394 LYS cc_start: 0.8267 (mptt) cc_final: 0.8022 (mptp) REVERT: A 404 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7127 (mt-10) REVERT: A 484 TYR cc_start: 0.8423 (t80) cc_final: 0.7902 (t80) REVERT: A 587 MET cc_start: 0.7305 (mtt) cc_final: 0.6984 (mtt) REVERT: A 606 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7485 (tt0) REVERT: A 706 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.6595 (tp) outliers start: 12 outliers final: 8 residues processed: 77 average time/residue: 0.9343 time to fit residues: 76.3813 Evaluate side-chains 79 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 706 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 3 optimal weight: 0.0980 chunk 61 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 17 optimal weight: 0.4980 chunk 64 optimal weight: 0.4980 chunk 53 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 10 optimal weight: 0.4980 chunk 6 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.153427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.117717 restraints weight = 5938.498| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.00 r_work: 0.3263 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5424 Z= 0.113 Angle : 0.524 11.878 7375 Z= 0.265 Chirality : 0.040 0.156 843 Planarity : 0.004 0.033 902 Dihedral : 3.924 18.879 702 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.43 % Allowed : 20.45 % Favored : 77.12 % 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: 1.01 (0.35), residues: 644 helix: 1.69 (0.26), residues: 431 sheet: -1.93 (1.26), residues: 17 loop : -1.44 (0.47), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 418 HIS 0.002 0.000 HIS A 214 PHE 0.011 0.001 PHE A 720 TYR 0.018 0.001 TYR A 285 ARG 0.001 0.000 ARG A 417 Details of bonding type rmsd hydrogen bonds : bond 0.03517 ( 326) hydrogen bonds : angle 4.24355 ( 936) covalent geometry : bond 0.00245 ( 5424) covalent geometry : angle 0.52390 ( 7375) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.611 Fit side-chains REVERT: A 53 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.7244 (mmm) REVERT: A 127 GLN cc_start: 0.8099 (mt0) cc_final: 0.7828 (mt0) REVERT: A 159 CYS cc_start: 0.8247 (m) cc_final: 0.7443 (t) REVERT: A 212 ARG cc_start: 0.6669 (mpt180) cc_final: 0.6323 (ttp80) REVERT: A 250 ASP cc_start: 0.7660 (t0) cc_final: 0.7449 (t0) REVERT: A 318 GLU cc_start: 0.6254 (tm-30) cc_final: 0.5720 (pt0) REVERT: A 347 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7916 (mp) REVERT: A 394 LYS cc_start: 0.8277 (mptt) cc_final: 0.8027 (mptp) REVERT: A 402 ASP cc_start: 0.7870 (t70) cc_final: 0.7381 (t70) REVERT: A 404 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7266 (mt-10) REVERT: A 587 MET cc_start: 0.7280 (mtt) cc_final: 0.6960 (mtt) REVERT: A 706 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.6567 (tp) outliers start: 14 outliers final: 10 residues processed: 80 average time/residue: 0.8220 time to fit residues: 70.0898 Evaluate side-chains 82 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 706 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 3 optimal weight: 0.0870 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.150933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.114990 restraints weight = 6032.277| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.00 r_work: 0.3230 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5424 Z= 0.146 Angle : 0.555 11.054 7375 Z= 0.281 Chirality : 0.041 0.162 843 Planarity : 0.004 0.033 902 Dihedral : 4.060 19.617 702 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.95 % Allowed : 20.10 % Favored : 76.95 % 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: 0.83 (0.35), residues: 644 helix: 1.46 (0.25), residues: 441 sheet: -2.01 (1.22), residues: 17 loop : -1.41 (0.49), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 418 HIS 0.002 0.001 HIS A 214 PHE 0.021 0.001 PHE A 155 TYR 0.031 0.002 TYR A 362 ARG 0.002 0.000 ARG A 417 Details of bonding type rmsd hydrogen bonds : bond 0.03763 ( 326) hydrogen bonds : angle 4.34542 ( 936) covalent geometry : bond 0.00341 ( 5424) covalent geometry : angle 0.55475 ( 7375) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4184.44 seconds wall clock time: 72 minutes 11.61 seconds (4331.61 seconds total)