Starting phenix.real_space_refine on Thu Nov 14 06:57:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wg3_37501/11_2024/8wg3_37501.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wg3_37501/11_2024/8wg3_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wg3_37501/11_2024/8wg3_37501.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wg3_37501/11_2024/8wg3_37501.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wg3_37501/11_2024/8wg3_37501.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wg3_37501/11_2024/8wg3_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-5513/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: 3.35, per 1000 atoms: 0.73 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: 1.31 Conformation dependent library (CDL) restraints added in 526.0 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: 0.45 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: 1.26 Time building geometry restraints manager: 1.47 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: 0.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.260 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.860 ------------------------------------------------------------------------------- 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 : 0.525 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: 0.1769 time to fit residues: 28.7960 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 : 0.503 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 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 : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8755 (m) cc_final: 0.8362 (p) REVERT: A 45 LEU cc_start: 0.7487 (tp) cc_final: 0.7126 (tp) REVERT: A 48 ASP cc_start: 0.8399 (m-30) cc_final: 0.8042 (m-30) REVERT: A 53 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6954 (tm) REVERT: A 181 ASP cc_start: 0.8198 (m-30) cc_final: 0.7688 (t0) REVERT: A 184 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7823 (mm-30) REVERT: A 185 ASN cc_start: 0.8049 (t0) cc_final: 0.7660 (t0) REVERT: A 186 ASN cc_start: 0.7753 (t0) cc_final: 0.7542 (t0) REVERT: A 261 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7624 (mm-30) REVERT: A 262 GLU cc_start: 0.8314 (tp30) cc_final: 0.7631 (tm-30) REVERT: A 414 ASP cc_start: 0.7199 (OUTLIER) cc_final: 0.6962 (p0) REVERT: A 446 PHE cc_start: 0.7873 (t80) cc_final: 0.7587 (t80) REVERT: A 587 ARG cc_start: 0.7446 (tpt-90) cc_final: 0.7117 (mmm160) REVERT: A 652 MET cc_start: 0.7872 (mmt) cc_final: 0.7449 (mmt) REVERT: A 659 ASP cc_start: 0.7941 (m-30) cc_final: 0.7662 (m-30) REVERT: A 674 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.6462 (mmtm) REVERT: A 712 PHE cc_start: 0.8169 (t80) cc_final: 0.7962 (t80) REVERT: A 720 THR cc_start: 0.8673 (m) cc_final: 0.7976 (p) outliers start: 13 outliers final: 4 residues processed: 124 average time/residue: 0.1525 time to fit residues: 24.4742 Evaluate side-chains 101 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 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 27 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 chunk 43 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4722 Z= 0.193 Angle : 0.665 8.264 6426 Z= 0.334 Chirality : 0.042 0.185 734 Planarity : 0.004 0.037 758 Dihedral : 13.062 175.440 856 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.51 % Allowed : 14.43 % Favored : 82.06 % 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: 0.90 (0.37), residues: 533 helix: 1.33 (0.28), residues: 334 sheet: 0.73 (1.26), residues: 17 loop : -0.73 (0.48), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 485 HIS 0.006 0.001 HIS A 157 PHE 0.016 0.002 PHE A 154 TYR 0.015 0.001 TYR A 637 ARG 0.002 0.000 ARG A 134 *********************** 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 114 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8893 (m) cc_final: 0.8453 (p) REVERT: A 53 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.6997 (tm) REVERT: A 181 ASP cc_start: 0.8394 (m-30) cc_final: 0.7953 (t0) REVERT: A 185 ASN cc_start: 0.7606 (t0) cc_final: 0.7318 (t0) REVERT: A 261 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7647 (mm-30) REVERT: A 262 GLU cc_start: 0.8263 (tp30) cc_final: 0.7691 (tm-30) REVERT: A 414 ASP cc_start: 0.7069 (OUTLIER) cc_final: 0.6811 (p0) REVERT: A 446 PHE cc_start: 0.7810 (t80) cc_final: 0.7441 (t80) REVERT: A 500 PHE cc_start: 0.8186 (t80) cc_final: 0.7915 (t80) REVERT: A 501 PHE cc_start: 0.6331 (m-80) cc_final: 0.5948 (m-10) REVERT: A 628 MET cc_start: 0.7650 (mmm) cc_final: 0.7314 (mmm) REVERT: A 652 MET cc_start: 0.7691 (mmt) cc_final: 0.7252 (mmt) REVERT: A 674 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.6321 (mmtp) REVERT: A 720 THR cc_start: 0.8688 (m) cc_final: 0.8427 (p) outliers start: 17 outliers final: 9 residues processed: 109 average time/residue: 0.1637 time to fit residues: 22.8578 Evaluate side-chains 96 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 490 LEU 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 48 optimal weight: 0.6980 chunk 36 optimal weight: 0.0670 chunk 25 optimal weight: 0.0970 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 0.0060 chunk 32 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 overall best weight: 0.2932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.3915 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 : 0.605 7.736 6426 Z= 0.303 Chirality : 0.040 0.185 734 Planarity : 0.004 0.036 758 Dihedral : 12.474 175.209 856 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.09 % Allowed : 15.67 % Favored : 81.24 % 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: 1.35 (0.37), residues: 533 helix: 1.65 (0.29), residues: 335 sheet: 0.52 (1.19), residues: 17 loop : -0.43 (0.49), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 407 HIS 0.004 0.001 HIS A 367 PHE 0.013 0.001 PHE A 59 TYR 0.011 0.001 TYR A 637 ARG 0.002 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 102 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8773 (m) cc_final: 0.8197 (p) REVERT: A 53 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6891 (tm) REVERT: A 181 ASP cc_start: 0.8513 (m-30) cc_final: 0.8124 (t0) REVERT: A 185 ASN cc_start: 0.7558 (t0) cc_final: 0.7214 (t0) REVERT: A 258 LYS cc_start: 0.7853 (tttt) cc_final: 0.7485 (tmmt) REVERT: A 262 GLU cc_start: 0.8184 (tp30) cc_final: 0.7639 (tm-30) REVERT: A 402 LEU cc_start: 0.8526 (mp) cc_final: 0.8292 (mt) REVERT: A 414 ASP cc_start: 0.7144 (OUTLIER) cc_final: 0.6885 (p0) REVERT: A 421 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7740 (mp0) REVERT: A 500 PHE cc_start: 0.8187 (t80) cc_final: 0.7911 (t80) REVERT: A 501 PHE cc_start: 0.6140 (m-80) cc_final: 0.5740 (m-10) REVERT: A 628 MET cc_start: 0.8103 (mmm) cc_final: 0.7476 (mmm) REVERT: A 652 MET cc_start: 0.7695 (mmt) cc_final: 0.7268 (mmt) REVERT: A 654 LEU cc_start: 0.7666 (mm) cc_final: 0.7231 (mm) REVERT: A 674 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.6013 (mmtp) REVERT: A 720 THR cc_start: 0.8730 (m) cc_final: 0.8425 (p) outliers start: 15 outliers final: 7 residues processed: 99 average time/residue: 0.1376 time to fit residues: 17.9698 Evaluate side-chains 95 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 490 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 44 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 0.0770 chunk 46 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 47 optimal weight: 0.0970 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 HIS A 571 ASN A 682 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.3987 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= 0.185 Angle : 0.609 7.914 6426 Z= 0.305 Chirality : 0.041 0.185 734 Planarity : 0.004 0.035 758 Dihedral : 12.348 168.996 856 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.89 % Allowed : 17.53 % Favored : 79.59 % 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: 1.61 (0.29), residues: 334 sheet: -0.00 (1.14), residues: 17 loop : -0.48 (0.49), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 407 HIS 0.004 0.001 HIS A 157 PHE 0.014 0.001 PHE A 52 TYR 0.011 0.001 TYR A 637 ARG 0.002 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 101 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8874 (m) cc_final: 0.8270 (p) REVERT: A 53 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.6957 (tm) REVERT: A 181 ASP cc_start: 0.8496 (m-30) cc_final: 0.8080 (t0) REVERT: A 185 ASN cc_start: 0.7682 (t0) cc_final: 0.7397 (t0) REVERT: A 258 LYS cc_start: 0.7790 (tttt) cc_final: 0.7407 (tmmt) REVERT: A 261 GLU cc_start: 0.8360 (mt-10) cc_final: 0.7764 (mm-30) REVERT: A 262 GLU cc_start: 0.8315 (tp30) cc_final: 0.7834 (tm-30) REVERT: A 367 HIS cc_start: 0.7105 (p90) cc_final: 0.6902 (p90) REVERT: A 400 GLU cc_start: 0.7797 (tt0) cc_final: 0.7578 (tm-30) REVERT: A 402 LEU cc_start: 0.8832 (mp) cc_final: 0.8467 (mt) REVERT: A 414 ASP cc_start: 0.7124 (OUTLIER) cc_final: 0.6846 (p0) REVERT: A 421 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7823 (mp0) REVERT: A 500 PHE cc_start: 0.8162 (t80) cc_final: 0.7956 (t80) REVERT: A 652 MET cc_start: 0.7713 (mmt) cc_final: 0.7280 (mmt) REVERT: A 654 LEU cc_start: 0.8152 (mm) cc_final: 0.7732 (mm) REVERT: A 674 LYS cc_start: 0.7541 (OUTLIER) cc_final: 0.5924 (mmtp) REVERT: A 720 THR cc_start: 0.8748 (m) cc_final: 0.8442 (p) outliers start: 14 outliers final: 9 residues processed: 96 average time/residue: 0.1456 time to fit residues: 18.5258 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 : 0.521 ------------------------------------------------------------------------------- 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 421 GLU Chi-restraints excluded: chain A residue 490 LEU 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 10 optimal weight: 3.9990 chunk 30 optimal weight: 0.0470 chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 24 optimal weight: 0.0570 chunk 4 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.4224 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= 0.166 Angle : 0.596 9.598 6426 Z= 0.294 Chirality : 0.040 0.190 734 Planarity : 0.004 0.035 758 Dihedral : 12.031 165.497 856 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.51 % Allowed : 17.53 % Favored : 78.97 % 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: 1.40 (0.38), residues: 533 helix: 1.70 (0.29), residues: 334 sheet: 0.08 (1.16), residues: 17 loop : -0.38 (0.49), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 407 HIS 0.004 0.001 HIS A 157 PHE 0.013 0.001 PHE A 178 TYR 0.010 0.001 TYR A 637 ARG 0.001 0.000 ARG A 156 *********************** 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 102 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 ASP cc_start: 0.8334 (m-30) cc_final: 0.8094 (t0) REVERT: A 185 ASN cc_start: 0.7628 (t0) cc_final: 0.7383 (t0) REVERT: A 258 LYS cc_start: 0.7771 (tttt) cc_final: 0.7410 (tmmt) REVERT: A 261 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8060 (mm-30) REVERT: A 262 GLU cc_start: 0.8273 (tp30) cc_final: 0.7824 (tm-30) REVERT: A 400 GLU cc_start: 0.7673 (tt0) cc_final: 0.7415 (tm-30) REVERT: A 402 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8490 (mt) REVERT: A 414 ASP cc_start: 0.7118 (OUTLIER) cc_final: 0.6853 (p0) REVERT: A 652 MET cc_start: 0.7788 (mmt) cc_final: 0.7407 (mmt) REVERT: A 654 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7189 (mm) REVERT: A 674 LYS cc_start: 0.7543 (OUTLIER) cc_final: 0.5906 (mmtp) REVERT: A 720 THR cc_start: 0.8756 (m) cc_final: 0.8409 (p) outliers start: 17 outliers final: 11 residues processed: 94 average time/residue: 0.1421 time to fit residues: 17.6987 Evaluate side-chains 102 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 402 LEU Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 490 LEU 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 672 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 29 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4722 Z= 0.268 Angle : 0.654 7.821 6426 Z= 0.331 Chirality : 0.043 0.182 734 Planarity : 0.004 0.035 758 Dihedral : 12.411 163.169 856 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.51 % Allowed : 17.32 % 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: 0.93 (0.37), residues: 533 helix: 1.36 (0.29), residues: 332 sheet: -0.34 (1.16), residues: 17 loop : -0.58 (0.47), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 505 HIS 0.007 0.001 HIS A 157 PHE 0.021 0.002 PHE A 52 TYR 0.014 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 100 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8990 (m) cc_final: 0.8638 (p) REVERT: A 181 ASP cc_start: 0.8387 (m-30) cc_final: 0.7725 (t0) REVERT: A 258 LYS cc_start: 0.7793 (tttt) cc_final: 0.7426 (tmmt) REVERT: A 262 GLU cc_start: 0.8186 (tp30) cc_final: 0.7834 (tm-30) REVERT: A 400 GLU cc_start: 0.7684 (tt0) cc_final: 0.7394 (tm-30) REVERT: A 402 LEU cc_start: 0.8863 (mp) cc_final: 0.8528 (mt) REVERT: A 414 ASP cc_start: 0.7010 (OUTLIER) cc_final: 0.6729 (p0) REVERT: A 652 MET cc_start: 0.7850 (mmt) cc_final: 0.7474 (mmt) REVERT: A 654 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7717 (mm) REVERT: A 674 LYS cc_start: 0.7500 (OUTLIER) cc_final: 0.5825 (mmtp) REVERT: A 720 THR cc_start: 0.8739 (m) cc_final: 0.8409 (p) outliers start: 17 outliers final: 12 residues processed: 92 average time/residue: 0.1407 time to fit residues: 17.1669 Evaluate side-chains 96 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 490 LEU 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 674 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 HIS A 406 ASN ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.4273 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= 0.202 Angle : 0.623 10.924 6426 Z= 0.311 Chirality : 0.041 0.192 734 Planarity : 0.004 0.036 758 Dihedral : 12.208 162.415 856 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.71 % Allowed : 18.14 % 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: 1.10 (0.37), residues: 533 helix: 1.49 (0.29), residues: 334 sheet: -0.40 (1.20), residues: 17 loop : -0.50 (0.48), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 505 HIS 0.005 0.001 HIS A 157 PHE 0.015 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 102 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8887 (m) cc_final: 0.8499 (p) REVERT: A 181 ASP cc_start: 0.8361 (m-30) cc_final: 0.7836 (t0) REVERT: A 258 LYS cc_start: 0.7778 (tttt) cc_final: 0.7420 (tmmt) REVERT: A 262 GLU cc_start: 0.8132 (tp30) cc_final: 0.7773 (tm-30) REVERT: A 400 GLU cc_start: 0.7758 (tt0) cc_final: 0.7396 (tm-30) REVERT: A 402 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8478 (mt) REVERT: A 414 ASP cc_start: 0.7025 (OUTLIER) cc_final: 0.6757 (p0) REVERT: A 652 MET cc_start: 0.7784 (mmt) cc_final: 0.7402 (mmt) REVERT: A 654 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7721 (mm) REVERT: A 674 LYS cc_start: 0.7525 (OUTLIER) cc_final: 0.5970 (mmtp) REVERT: A 720 THR cc_start: 0.8745 (m) cc_final: 0.8432 (p) outliers start: 18 outliers final: 12 residues processed: 93 average time/residue: 0.1412 time to fit residues: 17.4136 Evaluate side-chains 104 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 402 LEU Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 490 LEU 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 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 14 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 0.0030 chunk 51 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 53 optimal weight: 0.3980 chunk 49 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.4585 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= 0.162 Angle : 0.578 8.835 6426 Z= 0.289 Chirality : 0.039 0.195 734 Planarity : 0.004 0.036 758 Dihedral : 11.901 159.688 856 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % 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: 1.42 (0.38), residues: 533 helix: 1.72 (0.29), residues: 335 sheet: -0.17 (1.23), residues: 17 loop : -0.37 (0.50), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 407 HIS 0.004 0.001 HIS A 157 PHE 0.013 0.001 PHE A 697 TYR 0.011 0.001 TYR A 637 ARG 0.002 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 107 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8819 (m) cc_final: 0.8376 (p) REVERT: A 181 ASP cc_start: 0.8331 (m-30) cc_final: 0.7817 (t0) REVERT: A 258 LYS cc_start: 0.7649 (tttt) cc_final: 0.7299 (tmmt) REVERT: A 262 GLU cc_start: 0.8081 (tp30) cc_final: 0.7730 (tm-30) REVERT: A 367 HIS cc_start: 0.6750 (p90) cc_final: 0.6476 (p90) REVERT: A 400 GLU cc_start: 0.7397 (tt0) cc_final: 0.7058 (tm-30) REVERT: A 402 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8511 (mt) REVERT: A 414 ASP cc_start: 0.7045 (OUTLIER) cc_final: 0.6767 (p0) REVERT: A 459 ASP cc_start: 0.6707 (m-30) cc_final: 0.6504 (m-30) REVERT: A 652 MET cc_start: 0.7774 (mmt) cc_final: 0.7397 (mmt) REVERT: A 654 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7524 (mm) REVERT: A 674 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.6145 (mmtp) REVERT: A 720 THR cc_start: 0.8756 (m) cc_final: 0.8446 (p) outliers start: 13 outliers final: 9 residues processed: 100 average time/residue: 0.1387 time to fit residues: 18.5548 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 : 0.465 ------------------------------------------------------------------------------- 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 402 LEU Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 490 LEU 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 674 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 0.0370 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.4602 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= 0.175 Angle : 0.613 10.871 6426 Z= 0.306 Chirality : 0.041 0.202 734 Planarity : 0.004 0.036 758 Dihedral : 11.697 156.674 856 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % 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: 1.47 (0.38), residues: 533 helix: 1.77 (0.29), residues: 335 sheet: -0.15 (1.24), residues: 17 loop : -0.36 (0.50), residues: 181 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 0.016 0.001 PHE A 178 TYR 0.009 0.001 TYR A 637 ARG 0.002 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 100 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8823 (m) cc_final: 0.8356 (p) REVERT: A 181 ASP cc_start: 0.8307 (m-30) cc_final: 0.7783 (t0) REVERT: A 258 LYS cc_start: 0.7580 (tttt) cc_final: 0.7225 (tmmt) REVERT: A 262 GLU cc_start: 0.8048 (tp30) cc_final: 0.7699 (tm-30) REVERT: A 367 HIS cc_start: 0.6762 (p90) cc_final: 0.6490 (p90) REVERT: A 400 GLU cc_start: 0.7364 (tt0) cc_final: 0.7043 (tm-30) REVERT: A 402 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8527 (mt) REVERT: A 414 ASP cc_start: 0.6992 (OUTLIER) cc_final: 0.6701 (p0) REVERT: A 652 MET cc_start: 0.7776 (mmt) cc_final: 0.7377 (mmt) REVERT: A 654 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7703 (mm) REVERT: A 674 LYS cc_start: 0.7523 (OUTLIER) cc_final: 0.5910 (mmtp) REVERT: A 720 THR cc_start: 0.8773 (m) cc_final: 0.8421 (p) outliers start: 14 outliers final: 10 residues processed: 94 average time/residue: 0.1445 time to fit residues: 18.1137 Evaluate side-chains 99 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 402 LEU Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 490 LEU 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 674 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.0270 chunk 5 optimal weight: 0.0570 chunk 7 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 28 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 overall best weight: 0.3556 ------------------------------------------------------------------------------- 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 ** 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 = 0.4147 r_free = 0.4147 target = 0.179478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.146782 restraints weight = 6332.503| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 1.93 r_work: 0.3682 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3574 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 4722 Z= 0.159 Angle : 0.581 8.521 6426 Z= 0.292 Chirality : 0.040 0.217 734 Planarity : 0.004 0.037 758 Dihedral : 11.126 150.952 856 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % 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: 1.57 (0.38), residues: 533 helix: 1.82 (0.29), residues: 340 sheet: 0.05 (1.26), residues: 17 loop : -0.34 (0.51), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 407 HIS 0.002 0.001 HIS A 150 PHE 0.013 0.001 PHE A 697 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: 1355.60 seconds wall clock time: 25 minutes 11.35 seconds (1511.35 seconds total)