Starting phenix.real_space_refine on Tue Feb 11 07:29:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wg3_37501/02_2025/8wg3_37501.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wg3_37501/02_2025/8wg3_37501.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wg3_37501/02_2025/8wg3_37501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wg3_37501/02_2025/8wg3_37501.map" model { file = "/net/cci-nas-00/data/ceres_data/8wg3_37501/02_2025/8wg3_37501.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wg3_37501/02_2025/8wg3_37501.cif" } resolution = 3.4 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= -0.002 sd= 0.074 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 P 1 5.49 5 S 37 5.16 5 C 3080 2.51 5 N 710 2.21 5 O 757 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4585 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4446 Classifications: {'peptide': 548} Link IDs: {'PTRANS': 22, 'TRANS': 525} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'P1L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 139 Unusual residues: {'LBN': 1, 'Y01': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 3.41, per 1000 atoms: 0.74 Number of scatterers: 4585 At special positions: 0 Unit cell: (90.2625, 79.3688, 91.8187, 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 37 16.00 P 1 15.00 O 757 8.00 N 710 7.00 C 3080 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 559 " distance=2.04 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: 1.23 Conformation dependent library (CDL) restraints added in 587.6 milliseconds 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1042 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 1 sheets defined 71.0% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 31 through 35 removed outlier: 3.664A pdb=" N GLY A 35 " --> pdb=" O VAL A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 39 removed outlier: 3.649A pdb=" N GLY A 39 " --> pdb=" O LEU A 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 36 through 39' Processing helix chain 'A' and resid 40 through 64 Processing helix chain 'A' and resid 126 through 132 removed outlier: 3.903A pdb=" N THR A 130 " --> pdb=" O P1L A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 145 Processing helix chain 'A' and resid 145 through 172 removed outlier: 3.749A pdb=" N VAL A 149 " --> pdb=" O GLY A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 Processing helix chain 'A' and resid 189 through 198 removed outlier: 5.940A pdb=" N ILE A 195 " --> pdb=" O ARG A 192 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ALA A 196 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 229 removed outlier: 4.284A pdb=" N HIS A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET A 223 " --> pdb=" O THR A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 264 removed outlier: 3.939A pdb=" N PHE A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 378 Processing helix chain 'A' and resid 398 through 402 Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 421 through 425 removed outlier: 3.595A pdb=" N ILE A 425 " --> pdb=" O HIS A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 457 removed outlier: 3.637A pdb=" N PHE A 446 " --> pdb=" O PHE A 442 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE A 447 " --> pdb=" O ILE A 443 " (cutoff:3.500A) Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 466 through 470 removed outlier: 3.627A pdb=" N LEU A 470 " --> pdb=" O VAL A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 477 Processing helix chain 'A' and resid 477 through 499 Proline residue: A 492 - end of helix removed outlier: 3.522A pdb=" N TYR A 497 " --> pdb=" O THR A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 503 removed outlier: 3.581A pdb=" N ALA A 503 " --> pdb=" O PHE A 500 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 500 through 503' Processing helix chain 'A' and resid 506 through 527 removed outlier: 3.877A pdb=" N HIS A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 536 Processing helix chain 'A' and resid 537 through 546 removed outlier: 4.164A pdb=" N PHE A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 565 Processing helix chain 'A' and resid 566 through 587 removed outlier: 3.617A pdb=" N VAL A 570 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 638 Processing helix chain 'A' and resid 643 through 666 removed outlier: 4.713A pdb=" N PHE A 647 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR A 664 " --> pdb=" O ARG A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 701 removed outlier: 3.630A pdb=" N SER A 678 " --> pdb=" O LYS A 674 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 681 " --> pdb=" O HIS A 677 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASN A 682 " --> pdb=" O SER A 678 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A 683 " --> pdb=" O GLY A 679 " (cutoff:3.500A) Proline residue: A 688 - end of helix Processing helix chain 'A' and resid 707 through 726 Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 275 removed outlier: 4.708A pdb=" N MET A 361 " --> pdb=" O CYS A 275 " (cutoff:3.500A) 263 hydrogen bonds defined for protein. 747 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: 1.33 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 697 1.32 - 1.45: 1393 1.45 - 1.58: 2576 1.58 - 1.71: 2 1.71 - 1.84: 54 Bond restraints: 4722 Sorted by residual: bond pdb=" CE1 HIS A 656 " pdb=" NE2 HIS A 656 " ideal model delta sigma weight residual 1.321 1.268 0.053 1.00e-02 1.00e+04 2.81e+01 bond pdb=" CG HIS A 504 " pdb=" CD2 HIS A 504 " ideal model delta sigma weight residual 1.354 1.306 0.048 1.10e-02 8.26e+03 1.87e+01 bond pdb=" CG HIS A 656 " pdb=" CD2 HIS A 656 " ideal model delta sigma weight residual 1.354 1.307 0.047 1.10e-02 8.26e+03 1.86e+01 bond pdb=" CA SER A 210 " pdb=" CB SER A 210 " ideal model delta sigma weight residual 1.529 1.474 0.055 1.55e-02 4.16e+03 1.24e+01 bond pdb=" CA SER A 498 " pdb=" CB SER A 498 " ideal model delta sigma weight residual 1.528 1.482 0.046 1.66e-02 3.63e+03 7.70e+00 ... (remaining 4717 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 5457 2.04 - 4.09: 868 4.09 - 6.13: 92 6.13 - 8.17: 6 8.17 - 10.21: 3 Bond angle restraints: 6426 Sorted by residual: angle pdb=" CA PHE A 52 " pdb=" CB PHE A 52 " pdb=" CG PHE A 52 " ideal model delta sigma weight residual 113.80 121.36 -7.56 1.00e+00 1.00e+00 5.72e+01 angle pdb=" CA ASP A 459 " pdb=" CB ASP A 459 " pdb=" CG ASP A 459 " ideal model delta sigma weight residual 112.60 117.97 -5.37 1.00e+00 1.00e+00 2.88e+01 angle pdb=" CA PHE A 712 " pdb=" CB PHE A 712 " pdb=" CG PHE A 712 " ideal model delta sigma weight residual 113.80 118.86 -5.06 1.00e+00 1.00e+00 2.56e+01 angle pdb=" C THR A 464 " pdb=" CA THR A 464 " pdb=" CB THR A 464 " ideal model delta sigma weight residual 111.86 118.60 -6.74 1.34e+00 5.57e-01 2.53e+01 angle pdb=" CA HIS A 157 " pdb=" CB HIS A 157 " pdb=" CG HIS A 157 " ideal model delta sigma weight residual 113.80 109.24 4.56 1.00e+00 1.00e+00 2.08e+01 ... (remaining 6421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.42: 2797 35.42 - 70.84: 76 70.84 - 106.25: 3 106.25 - 141.67: 4 141.67 - 177.09: 2 Dihedral angle restraints: 2882 sinusoidal: 1272 harmonic: 1610 Sorted by residual: dihedral pdb=" CA TRP A 407 " pdb=" C TRP A 407 " pdb=" N THR A 408 " pdb=" CA THR A 408 " ideal model delta harmonic sigma weight residual 180.00 151.72 28.28 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA LYS A 383 " pdb=" C LYS A 383 " pdb=" N CYS A 384 " pdb=" CA CYS A 384 " ideal model delta harmonic sigma weight residual -180.00 -151.82 -28.18 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA CYS A 398 " pdb=" C CYS A 398 " pdb=" N SER A 399 " pdb=" CA SER A 399 " ideal model delta harmonic sigma weight residual -180.00 -154.70 -25.30 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 2879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 357 0.056 - 0.111: 238 0.111 - 0.167: 100 0.167 - 0.222: 33 0.222 - 0.278: 6 Chirality restraints: 734 Sorted by residual: chirality pdb=" CA ASN A 662 " pdb=" N ASN A 662 " pdb=" C ASN A 662 " pdb=" CB ASN A 662 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA THR A 464 " pdb=" N THR A 464 " pdb=" C THR A 464 " pdb=" CB THR A 464 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA SER A 737 " pdb=" N SER A 737 " pdb=" C SER A 737 " pdb=" CB SER A 737 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 731 not shown) Planarity restraints: 758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 485 " -0.060 2.00e-02 2.50e+03 2.90e-02 2.11e+01 pdb=" CG TRP A 485 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP A 485 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP A 485 " 0.014 2.00e-02 2.50e+03 pdb=" NE1 TRP A 485 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 485 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 485 " 0.027 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 485 " -0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 485 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 485 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 569 " 0.049 2.00e-02 2.50e+03 3.30e-02 1.91e+01 pdb=" CG PHE A 569 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE A 569 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 569 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE A 569 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 569 " 0.022 2.00e-02 2.50e+03 pdb=" CZ PHE A 569 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 637 " -0.055 2.00e-02 2.50e+03 2.93e-02 1.71e+01 pdb=" CG TYR A 637 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR A 637 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 637 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR A 637 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 637 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 637 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 637 " -0.025 2.00e-02 2.50e+03 ... (remaining 755 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 2335 3.00 - 3.48: 4769 3.48 - 3.95: 7045 3.95 - 4.43: 8133 4.43 - 4.90: 13249 Nonbonded interactions: 35531 Sorted by model distance: nonbonded pdb=" N VAL A 463 " pdb=" O VAL A 463 " model vdw 2.528 2.496 nonbonded pdb=" O LEU A 527 " pdb=" OG SER A 531 " model vdw 2.530 3.040 nonbonded pdb=" O THR A 632 " pdb=" OG1 THR A 636 " model vdw 2.537 3.040 nonbonded pdb=" N THR A 506 " pdb=" OG1 THR A 506 " model vdw 2.555 2.496 nonbonded pdb=" N PHE A 561 " pdb=" O PHE A 561 " model vdw 2.556 2.496 ... (remaining 35526 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: 0.150 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.250 Find NCS groups from input model: 0.050 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 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 : 0.009 0.055 4722 Z= 0.581 Angle : 1.474 10.213 6426 Z= 0.965 Chirality : 0.084 0.278 734 Planarity : 0.012 0.118 758 Dihedral : 16.488 177.090 1837 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 0.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.30 % Allowed : 6.80 % Favored : 89.90 % Cbeta Deviations : 0.19 % 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: -2.32 (0.33), residues: 533 helix: -1.76 (0.23), residues: 323 sheet: 1.12 (1.44), residues: 16 loop : -1.04 (0.48), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.010 TRP A 485 HIS 0.020 0.005 HIS A 739 PHE 0.063 0.008 PHE A 569 TYR 0.055 0.009 TYR A 637 ARG 0.027 0.003 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.6916 (mm) REVERT: A 44 VAL cc_start: 0.8417 (t) cc_final: 0.7954 (p) REVERT: A 50 MET cc_start: 0.7946 (ttt) cc_final: 0.7719 (tpt) REVERT: A 181 ASP cc_start: 0.8361 (m-30) cc_final: 0.7901 (t0) REVERT: A 184 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7695 (mm-30) REVERT: A 185 ASN cc_start: 0.6858 (t0) cc_final: 0.6615 (t0) REVERT: A 189 SER cc_start: 0.9020 (t) cc_final: 0.8710 (p) REVERT: A 261 GLU cc_start: 0.8535 (mt-10) cc_final: 0.7948 (tp30) REVERT: A 262 GLU cc_start: 0.8456 (tp30) cc_final: 0.7805 (tm-30) REVERT: A 367 HIS cc_start: 0.7199 (p-80) cc_final: 0.6952 (p90) REVERT: A 400 GLU cc_start: 0.8677 (tt0) cc_final: 0.8295 (tm-30) REVERT: A 458 MET cc_start: 0.7368 (mmm) cc_final: 0.7079 (mmm) REVERT: A 501 PHE cc_start: 0.6805 (m-80) cc_final: 0.6287 (m-10) REVERT: A 502 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7184 (mt-10) REVERT: A 512 ARG cc_start: 0.8326 (ttt-90) cc_final: 0.7810 (mtm110) REVERT: A 519 TYR cc_start: 0.9268 (t80) cc_final: 0.8919 (t80) REVERT: A 583 MET cc_start: 0.8712 (mmm) cc_final: 0.8415 (tpt) REVERT: A 587 ARG cc_start: 0.7620 (tpt-90) cc_final: 0.7331 (mmm160) REVERT: A 619 GLN cc_start: 0.8324 (mm-40) cc_final: 0.8122 (mm-40) REVERT: A 652 MET cc_start: 0.8232 (mmt) cc_final: 0.7815 (mmt) REVERT: A 712 PHE cc_start: 0.8161 (t80) cc_final: 0.7841 (t80) outliers start: 16 outliers final: 7 residues processed: 128 average time/residue: 0.1859 time to fit residues: 30.0287 Evaluate side-chains 95 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 206 TRP Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 695 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 0.0370 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 0.0270 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 31 optimal weight: 0.0980 chunk 49 optimal weight: 0.8980 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 ASN A 571 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.175433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.142584 restraints weight = 6272.798| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 1.91 r_work: 0.3626 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4722 Z= 0.180 Angle : 0.719 9.186 6426 Z= 0.362 Chirality : 0.042 0.208 734 Planarity : 0.005 0.038 758 Dihedral : 13.535 175.508 864 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.68 % Allowed : 12.16 % Favored : 85.15 % 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: 0.45 (0.37), residues: 533 helix: 0.90 (0.28), residues: 336 sheet: 1.20 (1.34), residues: 17 loop : -0.84 (0.49), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 407 HIS 0.005 0.001 HIS A 516 PHE 0.019 0.002 PHE A 154 TYR 0.016 0.001 TYR A 637 ARG 0.002 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8986 (m) cc_final: 0.8554 (p) REVERT: A 53 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7354 (tm) REVERT: A 62 LEU cc_start: 0.7114 (mt) cc_final: 0.6860 (mt) REVERT: A 147 ASP cc_start: 0.7619 (m-30) cc_final: 0.7392 (m-30) REVERT: A 185 ASN cc_start: 0.7608 (t0) cc_final: 0.7394 (t0) REVERT: A 261 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7445 (mm-30) REVERT: A 262 GLU cc_start: 0.8472 (tp30) cc_final: 0.7650 (tm-30) REVERT: A 414 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.7221 (p0) REVERT: A 490 LEU cc_start: 0.8627 (tt) cc_final: 0.8361 (mm) REVERT: A 585 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7709 (mm) REVERT: A 587 ARG cc_start: 0.7665 (tpt-90) cc_final: 0.7267 (mmm160) REVERT: A 628 MET cc_start: 0.7196 (mmm) cc_final: 0.6892 (mmm) REVERT: A 652 MET cc_start: 0.7287 (mmt) cc_final: 0.6878 (mmt) REVERT: A 674 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.6681 (mmtm) REVERT: A 720 THR cc_start: 0.8748 (m) cc_final: 0.8437 (p) outliers start: 13 outliers final: 4 residues processed: 124 average time/residue: 0.1525 time to fit residues: 24.4237 Evaluate side-chains 96 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 206 TRP Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 674 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 41 optimal weight: 0.0060 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 ASN A 438 ASN A 504 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.175069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.142182 restraints weight = 6389.597| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.96 r_work: 0.3620 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4722 Z= 0.183 Angle : 0.658 8.149 6426 Z= 0.334 Chirality : 0.042 0.189 734 Planarity : 0.004 0.037 758 Dihedral : 12.971 175.605 856 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.30 % Allowed : 15.05 % Favored : 81.65 % 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: 1.02 (0.37), residues: 533 helix: 1.43 (0.28), residues: 334 sheet: 0.77 (1.26), residues: 17 loop : -0.69 (0.48), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 407 HIS 0.005 0.001 HIS A 157 PHE 0.016 0.002 PHE A 154 TYR 0.014 0.001 TYR A 637 ARG 0.002 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: A 31 THR cc_start: 0.8968 (m) cc_final: 0.8503 (p) REVERT: A 53 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7305 (tm) REVERT: A 134 ARG cc_start: 0.7630 (ttt180) cc_final: 0.7393 (ttt180) REVERT: A 185 ASN cc_start: 0.7328 (t0) cc_final: 0.6955 (t0) REVERT: A 258 LYS cc_start: 0.8221 (tttt) cc_final: 0.7795 (tmmt) REVERT: A 261 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7486 (mm-30) REVERT: A 262 GLU cc_start: 0.8349 (tp30) cc_final: 0.7574 (tm-30) REVERT: A 414 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.7058 (p0) REVERT: A 628 MET cc_start: 0.7705 (mmm) cc_final: 0.6912 (mmm) REVERT: A 652 MET cc_start: 0.7114 (mmt) cc_final: 0.6666 (mmt) REVERT: A 674 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.6393 (mmtp) outliers start: 16 outliers final: 8 residues processed: 102 average time/residue: 0.1765 time to fit residues: 22.9344 Evaluate side-chains 92 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 206 TRP Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 736 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 1 optimal weight: 0.0970 chunk 34 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 42 optimal weight: 0.0060 chunk 25 optimal weight: 0.0970 chunk 37 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.3592 ------------------------------------------------------------------------------- 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 = 0.4131 r_free = 0.4131 target = 0.178233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.145813 restraints weight = 6388.366| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.93 r_work: 0.3660 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4722 Z= 0.153 Angle : 0.604 8.257 6426 Z= 0.303 Chirality : 0.040 0.191 734 Planarity : 0.004 0.035 758 Dihedral : 12.404 174.163 856 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.89 % Allowed : 15.26 % Favored : 81.86 % 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: 1.39 (0.38), residues: 533 helix: 1.70 (0.29), residues: 335 sheet: 0.76 (1.17), residues: 17 loop : -0.49 (0.49), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 407 HIS 0.003 0.001 HIS A 157 PHE 0.013 0.001 PHE A 59 TYR 0.011 0.001 TYR A 637 ARG 0.001 0.000 ARG A 512 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.527 Fit side-chains revert: symmetry clash REVERT: A 31 THR cc_start: 0.8965 (m) cc_final: 0.8343 (p) REVERT: A 53 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7230 (tm) REVERT: A 181 ASP cc_start: 0.8642 (t0) cc_final: 0.8324 (t0) REVERT: A 185 ASN cc_start: 0.7494 (t0) cc_final: 0.6827 (t0) REVERT: A 258 LYS cc_start: 0.8178 (tttt) cc_final: 0.7754 (tmmt) REVERT: A 262 GLU cc_start: 0.8151 (tp30) cc_final: 0.7715 (tm-30) REVERT: A 414 ASP cc_start: 0.7478 (OUTLIER) cc_final: 0.7057 (p0) REVERT: A 421 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7322 (mp0) REVERT: A 458 MET cc_start: 0.7487 (mmm) cc_final: 0.7261 (mmm) REVERT: A 501 PHE cc_start: 0.7010 (m-80) cc_final: 0.6536 (m-10) REVERT: A 652 MET cc_start: 0.7163 (mmt) cc_final: 0.6740 (mmt) REVERT: A 654 LEU cc_start: 0.8821 (mm) cc_final: 0.8382 (mp) REVERT: A 674 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.6392 (mmtp) outliers start: 14 outliers final: 6 residues processed: 99 average time/residue: 0.1384 time to fit residues: 18.1633 Evaluate side-chains 93 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 206 TRP Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 674 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 15 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 0.0070 chunk 9 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 16 optimal weight: 0.0980 overall best weight: 0.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.176991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.144280 restraints weight = 6432.442| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.95 r_work: 0.3636 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4722 Z= 0.171 Angle : 0.600 6.905 6426 Z= 0.303 Chirality : 0.041 0.190 734 Planarity : 0.004 0.034 758 Dihedral : 12.216 168.084 856 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.27 % Allowed : 18.56 % Favored : 79.18 % 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: 1.33 (0.38), residues: 533 helix: 1.69 (0.29), residues: 334 sheet: 0.19 (1.14), residues: 17 loop : -0.53 (0.49), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 407 HIS 0.004 0.001 HIS A 157 PHE 0.014 0.001 PHE A 52 TYR 0.010 0.001 TYR A 637 ARG 0.001 0.000 ARG A 512 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 31 THR cc_start: 0.8973 (m) cc_final: 0.8328 (p) REVERT: A 53 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7268 (tm) REVERT: A 181 ASP cc_start: 0.8656 (t0) cc_final: 0.8274 (t0) REVERT: A 185 ASN cc_start: 0.7129 (t0) cc_final: 0.6745 (t0) REVERT: A 258 LYS cc_start: 0.8169 (tttt) cc_final: 0.7725 (tmmt) REVERT: A 261 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7626 (mm-30) REVERT: A 262 GLU cc_start: 0.8344 (tp30) cc_final: 0.7941 (tm-30) REVERT: A 501 PHE cc_start: 0.7001 (m-80) cc_final: 0.6547 (m-10) REVERT: A 652 MET cc_start: 0.7097 (mmt) cc_final: 0.6705 (mmt) REVERT: A 654 LEU cc_start: 0.9078 (mm) cc_final: 0.8628 (mm) REVERT: A 674 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.6153 (mmtp) outliers start: 11 outliers final: 8 residues processed: 95 average time/residue: 0.1422 time to fit residues: 17.8588 Evaluate side-chains 89 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 206 TRP Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 674 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 15 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.195910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.165997 restraints weight = 6281.659| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 1.81 r_work: 0.3903 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3796 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4722 Z= 0.187 Angle : 0.610 9.879 6426 Z= 0.303 Chirality : 0.041 0.191 734 Planarity : 0.004 0.034 758 Dihedral : 12.217 164.997 856 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.09 % Allowed : 18.76 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.37), residues: 533 helix: 1.63 (0.29), residues: 335 sheet: -0.13 (1.12), residues: 17 loop : -0.51 (0.49), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 694 HIS 0.006 0.001 HIS A 157 PHE 0.014 0.001 PHE A 52 TYR 0.011 0.001 TYR A 637 ARG 0.001 0.000 ARG A 702 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: A 185 ASN cc_start: 0.7039 (t0) cc_final: 0.6753 (t0) REVERT: A 258 LYS cc_start: 0.8217 (tttt) cc_final: 0.7797 (tmmt) REVERT: A 261 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7835 (tp30) REVERT: A 414 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.7177 (p0) REVERT: A 501 PHE cc_start: 0.6711 (m-80) cc_final: 0.6405 (m-10) REVERT: A 652 MET cc_start: 0.7087 (mmt) cc_final: 0.6677 (mmt) REVERT: A 654 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8663 (mm) REVERT: A 674 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.6583 (mmtp) outliers start: 15 outliers final: 10 residues processed: 92 average time/residue: 0.1416 time to fit residues: 17.2474 Evaluate side-chains 94 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 206 TRP Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 674 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.4095 r_free = 0.4095 target = 0.176182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.144101 restraints weight = 6218.417| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.87 r_work: 0.3624 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 4722 Z= 0.311 Angle : 0.694 8.393 6426 Z= 0.351 Chirality : 0.045 0.183 734 Planarity : 0.005 0.036 758 Dihedral : 12.578 163.828 856 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.30 % Allowed : 18.76 % Favored : 77.94 % 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: 0.63 (0.36), residues: 533 helix: 1.20 (0.29), residues: 332 sheet: -0.61 (1.16), residues: 17 loop : -0.87 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 505 HIS 0.006 0.002 HIS A 157 PHE 0.025 0.002 PHE A 52 TYR 0.015 0.001 TYR A 637 ARG 0.003 0.000 ARG A 702 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.9115 (m) cc_final: 0.8734 (p) REVERT: A 185 ASN cc_start: 0.7125 (t0) cc_final: 0.6910 (t0) REVERT: A 258 LYS cc_start: 0.8170 (tttt) cc_final: 0.7785 (tmmt) REVERT: A 501 PHE cc_start: 0.6889 (m-80) cc_final: 0.6389 (m-10) REVERT: A 652 MET cc_start: 0.7148 (mmt) cc_final: 0.6790 (mmt) REVERT: A 654 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8601 (mm) REVERT: A 674 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.6546 (mmtp) outliers start: 16 outliers final: 13 residues processed: 91 average time/residue: 0.1515 time to fit residues: 17.9445 Evaluate side-chains 98 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 206 TRP Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 674 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 22 optimal weight: 0.0040 chunk 3 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 39 optimal weight: 0.3980 chunk 38 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 683 GLN ** 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 = 0.4144 r_free = 0.4144 target = 0.181093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.149837 restraints weight = 6130.072| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 1.86 r_work: 0.3707 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4722 Z= 0.182 Angle : 0.618 10.752 6426 Z= 0.306 Chirality : 0.040 0.203 734 Planarity : 0.004 0.035 758 Dihedral : 12.225 162.168 856 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.68 % Allowed : 19.38 % Favored : 77.94 % 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: 1.05 (0.37), residues: 533 helix: 1.52 (0.29), residues: 334 sheet: -0.45 (1.19), residues: 17 loop : -0.68 (0.48), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 407 HIS 0.005 0.001 HIS A 157 PHE 0.014 0.001 PHE A 178 TYR 0.010 0.001 TYR A 637 ARG 0.001 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8963 (m) cc_final: 0.8565 (p) REVERT: A 258 LYS cc_start: 0.8157 (tttt) cc_final: 0.7813 (tmmt) REVERT: A 414 ASP cc_start: 0.7449 (OUTLIER) cc_final: 0.7013 (p0) REVERT: A 501 PHE cc_start: 0.6880 (m-80) cc_final: 0.6371 (m-10) REVERT: A 652 MET cc_start: 0.7100 (mmt) cc_final: 0.6739 (mmt) REVERT: A 654 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8614 (mm) REVERT: A 674 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.6521 (mmtp) outliers start: 13 outliers final: 10 residues processed: 90 average time/residue: 0.1454 time to fit residues: 17.3896 Evaluate side-chains 92 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 206 TRP Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 674 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 3 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 ASN ** A 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.179859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.148643 restraints weight = 6148.983| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 1.85 r_work: 0.3692 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4722 Z= 0.192 Angle : 0.611 8.144 6426 Z= 0.309 Chirality : 0.041 0.201 734 Planarity : 0.004 0.035 758 Dihedral : 12.027 159.628 856 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.89 % Allowed : 18.97 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.37), residues: 533 helix: 1.58 (0.29), residues: 331 sheet: -0.49 (1.21), residues: 17 loop : -0.64 (0.47), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 407 HIS 0.005 0.001 HIS A 157 PHE 0.015 0.001 PHE A 52 TYR 0.011 0.001 TYR A 637 ARG 0.001 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8953 (m) cc_final: 0.8514 (p) REVERT: A 258 LYS cc_start: 0.8046 (tttt) cc_final: 0.7685 (tmmt) REVERT: A 414 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.6988 (p0) REVERT: A 501 PHE cc_start: 0.6874 (m-80) cc_final: 0.6354 (m-10) REVERT: A 652 MET cc_start: 0.7110 (mmt) cc_final: 0.6759 (mmt) REVERT: A 654 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8616 (mm) REVERT: A 674 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.6271 (mmtp) outliers start: 14 outliers final: 10 residues processed: 92 average time/residue: 0.1395 time to fit residues: 16.9752 Evaluate side-chains 95 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 206 TRP Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 674 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 12 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 0.2980 chunk 48 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 GLN ** 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 = 0.4146 r_free = 0.4146 target = 0.180608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.149221 restraints weight = 6158.954| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 1.86 r_work: 0.3686 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4722 Z= 0.186 Angle : 0.623 11.159 6426 Z= 0.310 Chirality : 0.041 0.212 734 Planarity : 0.004 0.035 758 Dihedral : 11.731 156.249 856 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.68 % Allowed : 18.76 % Favored : 78.56 % 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: 1.21 (0.37), residues: 533 helix: 1.66 (0.29), residues: 332 sheet: -0.40 (1.22), residues: 17 loop : -0.63 (0.48), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 407 HIS 0.005 0.001 HIS A 157 PHE 0.016 0.001 PHE A 178 TYR 0.010 0.001 TYR A 637 ARG 0.001 0.000 ARG A 192 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: A 31 THR cc_start: 0.8947 (m) cc_final: 0.8482 (p) REVERT: A 258 LYS cc_start: 0.8042 (tttt) cc_final: 0.7660 (tmmt) REVERT: A 414 ASP cc_start: 0.7382 (OUTLIER) cc_final: 0.6938 (p0) REVERT: A 501 PHE cc_start: 0.7237 (m-80) cc_final: 0.6778 (m-10) REVERT: A 652 MET cc_start: 0.7103 (mmt) cc_final: 0.6755 (mmt) REVERT: A 654 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8606 (mm) REVERT: A 674 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.6266 (mmtp) outliers start: 13 outliers final: 10 residues processed: 92 average time/residue: 0.1383 time to fit residues: 17.0416 Evaluate side-chains 98 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 206 TRP Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 674 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 37 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 49 optimal weight: 0.0770 chunk 18 optimal weight: 0.1980 chunk 3 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 41 optimal weight: 0.0370 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 ASN ** A 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.184588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.153204 restraints weight = 6167.380| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 1.86 r_work: 0.3730 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3621 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 4722 Z= 0.160 Angle : 0.591 8.217 6426 Z= 0.296 Chirality : 0.040 0.207 734 Planarity : 0.004 0.036 758 Dihedral : 11.204 149.562 856 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.06 % Allowed : 19.38 % Favored : 78.56 % 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: 1.46 (0.38), residues: 533 helix: 1.82 (0.29), residues: 335 sheet: -0.09 (1.26), residues: 17 loop : -0.51 (0.49), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 407 HIS 0.003 0.001 HIS A 157 PHE 0.011 0.001 PHE A 52 TYR 0.011 0.001 TYR A 637 ARG 0.002 0.000 ARG A 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2650.55 seconds wall clock time: 47 minutes 39.14 seconds (2859.14 seconds total)