Starting phenix.real_space_refine on Fri Aug 22 15:05:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wg3_37501/08_2025/8wg3_37501.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wg3_37501/08_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_37501/08_2025/8wg3_37501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wg3_37501/08_2025/8wg3_37501.map" model { file = "/net/cci-nas-00/data/ceres_data/8wg3_37501/08_2025/8wg3_37501.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wg3_37501/08_2025/8wg3_37501.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.37, per 1000 atoms: 0.30 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: 0.43 Conformation dependent library (CDL) restraints added in 135.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.08 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: 0.57 Time building geometry restraints manager: 0.55 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: 0.360 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: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.840 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.640 ------------------------------------------------------------------------------- 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 4723 Z= 0.595 Angle : 1.474 10.213 6428 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.027 0.003 ARG A 156 TYR 0.055 0.009 TYR A 637 PHE 0.063 0.008 PHE A 569 TRP 0.060 0.010 TRP A 485 HIS 0.020 0.005 HIS A 739 Details of bonding type rmsd covalent geometry : bond 0.00908 ( 4722) covalent geometry : angle 1.47419 ( 6426) SS BOND : bond 0.01219 ( 1) SS BOND : angle 1.72417 ( 2) hydrogen bonds : bond 0.19564 ( 263) hydrogen bonds : angle 8.84995 ( 747) *********************** 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 : 0.114 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: 0.0657 time to fit residues: 10.6316 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 : 0.154 ------------------------------------------------------------------------------- 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 24 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 ASN A 571 ASN A 581 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.172302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.139241 restraints weight = 6511.068| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 1.94 r_work: 0.3580 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4723 Z= 0.159 Angle : 0.747 9.060 6428 Z= 0.376 Chirality : 0.044 0.214 734 Planarity : 0.005 0.038 758 Dihedral : 13.790 175.504 864 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.30 % Allowed : 12.37 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.37), residues: 533 helix: 0.67 (0.28), residues: 336 sheet: 0.96 (1.31), residues: 17 loop : -0.99 (0.49), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 702 TYR 0.017 0.001 TYR A 637 PHE 0.019 0.002 PHE A 154 TRP 0.022 0.002 TRP A 485 HIS 0.006 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 4722) covalent geometry : angle 0.74664 ( 6426) SS BOND : bond 0.00083 ( 1) SS BOND : angle 0.31939 ( 2) hydrogen bonds : bond 0.05069 ( 263) hydrogen bonds : angle 5.41760 ( 747) *********************** 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 124 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.9068 (m) cc_final: 0.8626 (p) REVERT: A 36 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.6972 (mm) REVERT: A 53 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7505 (tm) REVERT: A 181 ASP cc_start: 0.8219 (m-30) cc_final: 0.7864 (t0) REVERT: A 184 GLU cc_start: 0.8246 (mm-30) cc_final: 0.8015 (mm-30) REVERT: A 261 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7483 (mm-30) REVERT: A 446 PHE cc_start: 0.7462 (t80) cc_final: 0.7227 (t80) REVERT: A 628 MET cc_start: 0.7657 (mmm) cc_final: 0.7205 (mmm) REVERT: A 652 MET cc_start: 0.7365 (mmt) cc_final: 0.6891 (mmt) REVERT: A 674 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.6749 (mmtm) REVERT: A 720 THR cc_start: 0.8795 (m) cc_final: 0.8431 (p) outliers start: 16 outliers final: 6 residues processed: 118 average time/residue: 0.0569 time to fit residues: 8.8171 Evaluate side-chains 92 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 43 THR 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 4 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 GLN A 504 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.170950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.137941 restraints weight = 6419.548| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.93 r_work: 0.3572 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4723 Z= 0.173 Angle : 0.709 8.559 6428 Z= 0.358 Chirality : 0.044 0.195 734 Planarity : 0.005 0.038 758 Dihedral : 13.557 174.331 858 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.92 % Allowed : 15.26 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.37), residues: 533 helix: 0.97 (0.28), residues: 337 sheet: 0.17 (1.27), residues: 17 loop : -0.93 (0.47), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 702 TYR 0.015 0.001 TYR A 637 PHE 0.019 0.002 PHE A 52 TRP 0.017 0.002 TRP A 485 HIS 0.006 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 4722) covalent geometry : angle 0.70893 ( 6426) SS BOND : bond 0.00090 ( 1) SS BOND : angle 0.48956 ( 2) hydrogen bonds : bond 0.05073 ( 263) hydrogen bonds : angle 5.11260 ( 747) *********************** 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 108 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.9102 (m) cc_final: 0.8616 (p) REVERT: A 36 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.6752 (mm) REVERT: A 53 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7439 (tm) REVERT: A 181 ASP cc_start: 0.8178 (m-30) cc_final: 0.7888 (t0) REVERT: A 261 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7636 (tp30) REVERT: A 262 GLU cc_start: 0.8467 (tp30) cc_final: 0.7719 (tm-30) REVERT: A 446 PHE cc_start: 0.7525 (t80) cc_final: 0.7193 (t80) REVERT: A 534 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8838 (mp) REVERT: A 628 MET cc_start: 0.7809 (mmm) cc_final: 0.7057 (mmm) REVERT: A 652 MET cc_start: 0.7256 (mmt) cc_final: 0.6830 (mmt) outliers start: 19 outliers final: 13 residues processed: 101 average time/residue: 0.0571 time to fit residues: 7.7028 Evaluate side-chains 93 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU 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 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 534 LEU Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 657 LEU 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 40 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 15 optimal weight: 0.0000 chunk 45 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 438 ASN ** 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 = 0.4089 r_free = 0.4089 target = 0.174789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.141963 restraints weight = 6454.010| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.95 r_work: 0.3626 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4723 Z= 0.123 Angle : 0.625 7.362 6428 Z= 0.315 Chirality : 0.041 0.192 734 Planarity : 0.004 0.037 758 Dihedral : 12.756 171.000 858 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.68 % Allowed : 16.91 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.37), residues: 533 helix: 1.43 (0.29), residues: 335 sheet: -0.04 (1.17), residues: 17 loop : -0.78 (0.48), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 512 TYR 0.010 0.001 TYR A 637 PHE 0.019 0.001 PHE A 59 TRP 0.015 0.002 TRP A 407 HIS 0.004 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 4722) covalent geometry : angle 0.62527 ( 6426) SS BOND : bond 0.00022 ( 1) SS BOND : angle 0.35987 ( 2) hydrogen bonds : bond 0.04374 ( 263) hydrogen bonds : angle 4.70951 ( 747) *********************** 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 100 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8996 (m) cc_final: 0.8337 (p) REVERT: A 53 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7276 (tm) REVERT: A 185 ASN cc_start: 0.8240 (t0) cc_final: 0.7375 (t0) REVERT: A 258 LYS cc_start: 0.8231 (tttt) cc_final: 0.7768 (tmmt) REVERT: A 261 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7538 (mm-30) REVERT: A 262 GLU cc_start: 0.8270 (tp30) cc_final: 0.7741 (tm-30) REVERT: A 402 LEU cc_start: 0.8633 (mp) cc_final: 0.8264 (mt) REVERT: A 414 ASP cc_start: 0.7494 (OUTLIER) cc_final: 0.7054 (p0) REVERT: A 421 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7403 (mp0) REVERT: A 490 LEU cc_start: 0.8673 (tt) cc_final: 0.8130 (mm) REVERT: A 652 MET cc_start: 0.7159 (mmt) cc_final: 0.6744 (mmt) REVERT: A 654 LEU cc_start: 0.8849 (mm) cc_final: 0.8445 (mm) REVERT: A 674 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.6330 (mmtp) outliers start: 13 outliers final: 7 residues processed: 96 average time/residue: 0.0482 time to fit residues: 6.2157 Evaluate side-chains 91 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.157 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 736 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 1 optimal weight: 0.0670 chunk 5 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 44 optimal weight: 0.1980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 HIS A 571 ASN A 682 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.194579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.165132 restraints weight = 6351.481| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 1.79 r_work: 0.3926 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3821 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4723 Z= 0.116 Angle : 0.589 7.716 6428 Z= 0.298 Chirality : 0.041 0.199 734 Planarity : 0.004 0.037 758 Dihedral : 12.271 167.695 856 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.68 % Allowed : 17.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.38), residues: 533 helix: 1.61 (0.29), residues: 335 sheet: -0.25 (1.17), residues: 17 loop : -0.66 (0.49), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 192 TYR 0.009 0.001 TYR A 637 PHE 0.013 0.001 PHE A 59 TRP 0.012 0.001 TRP A 407 HIS 0.004 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 4722) covalent geometry : angle 0.58941 ( 6426) SS BOND : bond 0.00615 ( 1) SS BOND : angle 0.39451 ( 2) hydrogen bonds : bond 0.04166 ( 263) hydrogen bonds : angle 4.57158 ( 747) *********************** 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: 13 poor density : 86 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7411 (tm) REVERT: A 185 ASN cc_start: 0.7862 (t0) cc_final: 0.7639 (t0) REVERT: A 258 LYS cc_start: 0.8261 (tttt) cc_final: 0.7842 (tmmt) REVERT: A 262 GLU cc_start: 0.8405 (tp30) cc_final: 0.7971 (tm-30) REVERT: A 402 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8457 (mt) REVERT: A 414 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7274 (p0) REVERT: A 501 PHE cc_start: 0.7186 (m-80) cc_final: 0.6784 (m-10) REVERT: A 652 MET cc_start: 0.6947 (mmt) cc_final: 0.6592 (mmt) REVERT: A 654 LEU cc_start: 0.8891 (mm) cc_final: 0.8499 (mm) REVERT: A 674 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.6467 (mmtp) outliers start: 13 outliers final: 7 residues processed: 94 average time/residue: 0.0523 time to fit residues: 6.5527 Evaluate side-chains 93 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.141 ------------------------------------------------------------------------------- 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 584 ASP Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 736 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 26 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 HIS ** A 438 ASN ** 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 = 0.4325 r_free = 0.4325 target = 0.195415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.164012 restraints weight = 6477.427| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 1.95 r_work: 0.3881 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3772 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4723 Z= 0.131 Angle : 0.615 8.567 6428 Z= 0.307 Chirality : 0.041 0.192 734 Planarity : 0.004 0.036 758 Dihedral : 12.205 165.461 854 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.38), residues: 533 helix: 1.41 (0.29), residues: 340 sheet: -0.40 (1.17), residues: 17 loop : -0.78 (0.49), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 134 TYR 0.011 0.001 TYR A 22 PHE 0.014 0.001 PHE A 52 TRP 0.017 0.001 TRP A 407 HIS 0.005 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 4722) covalent geometry : angle 0.61507 ( 6426) SS BOND : bond 0.00073 ( 1) SS BOND : angle 0.46277 ( 2) hydrogen bonds : bond 0.04319 ( 263) hydrogen bonds : angle 4.58580 ( 747) *********************** 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 101 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8894 (m) cc_final: 0.8557 (p) REVERT: A 185 ASN cc_start: 0.7761 (t0) cc_final: 0.7382 (t0) REVERT: A 258 LYS cc_start: 0.8238 (tttt) cc_final: 0.7809 (tmmt) REVERT: A 262 GLU cc_start: 0.8180 (tp30) cc_final: 0.7976 (tm-30) REVERT: A 402 LEU cc_start: 0.8985 (mp) cc_final: 0.8627 (mt) REVERT: A 414 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7173 (p0) REVERT: A 420 TRP cc_start: 0.7158 (OUTLIER) cc_final: 0.6958 (m-10) REVERT: A 490 LEU cc_start: 0.8833 (tt) cc_final: 0.8626 (mm) REVERT: A 501 PHE cc_start: 0.6719 (m-80) cc_final: 0.6400 (m-10) REVERT: A 652 MET cc_start: 0.7080 (mmt) cc_final: 0.6690 (mmt) REVERT: A 654 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8648 (mm) REVERT: A 674 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.6487 (mmtp) outliers start: 15 outliers final: 8 residues processed: 96 average time/residue: 0.0523 time to fit residues: 6.5197 Evaluate side-chains 93 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.161 ------------------------------------------------------------------------------- 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 420 TRP Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 736 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 19 optimal weight: 20.0000 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 31 optimal weight: 0.0470 chunk 47 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 11 optimal weight: 0.2980 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4318 r_free = 0.4318 target = 0.194274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.164454 restraints weight = 6411.000| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 1.81 r_work: 0.3914 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3811 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4723 Z= 0.119 Angle : 0.609 9.690 6428 Z= 0.297 Chirality : 0.040 0.194 734 Planarity : 0.004 0.036 758 Dihedral : 11.951 162.888 854 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.89 % Allowed : 19.59 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.38), residues: 533 helix: 1.53 (0.29), residues: 340 sheet: -0.39 (1.23), residues: 17 loop : -0.71 (0.49), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 433 TYR 0.008 0.001 TYR A 519 PHE 0.013 0.001 PHE A 178 TRP 0.016 0.001 TRP A 407 HIS 0.004 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 4722) covalent geometry : angle 0.60869 ( 6426) SS BOND : bond 0.00048 ( 1) SS BOND : angle 0.38924 ( 2) hydrogen bonds : bond 0.04093 ( 263) hydrogen bonds : angle 4.45514 ( 747) *********************** 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 101 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8845 (m) cc_final: 0.8478 (p) REVERT: A 185 ASN cc_start: 0.7694 (t0) cc_final: 0.7336 (t0) REVERT: A 258 LYS cc_start: 0.8240 (tttt) cc_final: 0.7842 (tmmt) REVERT: A 262 GLU cc_start: 0.8294 (tp30) cc_final: 0.7944 (tm-30) REVERT: A 402 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8603 (mt) REVERT: A 414 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7199 (p0) REVERT: A 501 PHE cc_start: 0.6691 (m-80) cc_final: 0.6417 (m-10) REVERT: A 652 MET cc_start: 0.6924 (mmt) cc_final: 0.6558 (mmt) REVERT: A 654 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8714 (mm) REVERT: A 674 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.6629 (mmtp) outliers start: 14 outliers final: 8 residues processed: 96 average time/residue: 0.0575 time to fit residues: 7.1973 Evaluate side-chains 93 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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 523 ILE Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 736 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 12 optimal weight: 0.0040 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 0.0980 chunk 23 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.195939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.166363 restraints weight = 6474.836| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 1.83 r_work: 0.3943 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3839 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4723 Z= 0.114 Angle : 0.586 9.725 6428 Z= 0.292 Chirality : 0.040 0.197 734 Planarity : 0.004 0.036 758 Dihedral : 11.581 160.182 854 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.38), residues: 533 helix: 1.66 (0.29), residues: 341 sheet: -0.25 (1.27), residues: 17 loop : -0.55 (0.50), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 192 TYR 0.033 0.001 TYR A 519 PHE 0.012 0.001 PHE A 52 TRP 0.016 0.001 TRP A 407 HIS 0.003 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 4722) covalent geometry : angle 0.58573 ( 6426) SS BOND : bond 0.00059 ( 1) SS BOND : angle 0.33461 ( 2) hydrogen bonds : bond 0.03907 ( 263) hydrogen bonds : angle 4.32884 ( 747) *********************** 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 105 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8828 (m) cc_final: 0.8405 (p) REVERT: A 185 ASN cc_start: 0.7601 (t0) cc_final: 0.7300 (t0) REVERT: A 258 LYS cc_start: 0.8073 (tttt) cc_final: 0.7668 (tmmt) REVERT: A 402 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8486 (mt) REVERT: A 414 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.7157 (p0) REVERT: A 652 MET cc_start: 0.6948 (mmt) cc_final: 0.6570 (mmt) REVERT: A 654 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8520 (mm) REVERT: A 674 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.6332 (mmtp) outliers start: 16 outliers final: 7 residues processed: 99 average time/residue: 0.0575 time to fit residues: 7.5740 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 : 0.162 ------------------------------------------------------------------------------- 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 402 LEU Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 420 TRP Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 736 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 37 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 21 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.181108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.149853 restraints weight = 6139.160| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 1.87 r_work: 0.3704 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3596 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4723 Z= 0.132 Angle : 0.624 10.692 6428 Z= 0.309 Chirality : 0.041 0.197 734 Planarity : 0.004 0.035 758 Dihedral : 11.684 158.088 854 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.38), residues: 533 helix: 1.57 (0.29), residues: 341 sheet: -0.45 (1.24), residues: 17 loop : -0.60 (0.50), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 512 TYR 0.034 0.001 TYR A 519 PHE 0.023 0.001 PHE A 712 TRP 0.012 0.001 TRP A 505 HIS 0.003 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 4722) covalent geometry : angle 0.62343 ( 6426) SS BOND : bond 0.00142 ( 1) SS BOND : angle 0.88552 ( 2) hydrogen bonds : bond 0.04083 ( 263) hydrogen bonds : angle 4.43281 ( 747) *********************** 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 97 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8955 (m) cc_final: 0.8471 (p) REVERT: A 185 ASN cc_start: 0.7286 (t0) cc_final: 0.6883 (t0) REVERT: A 258 LYS cc_start: 0.8019 (tttt) cc_final: 0.7630 (tmmt) REVERT: A 402 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8472 (mt) REVERT: A 414 ASP cc_start: 0.7385 (OUTLIER) cc_final: 0.6951 (p0) REVERT: A 652 MET cc_start: 0.7133 (mmt) cc_final: 0.6785 (mmt) REVERT: A 654 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8680 (mm) REVERT: A 674 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.6269 (mmtp) outliers start: 13 outliers final: 8 residues processed: 92 average time/residue: 0.0522 time to fit residues: 6.3574 Evaluate side-chains 98 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.109 ------------------------------------------------------------------------------- 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 654 LEU Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 736 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 37 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.179096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.147501 restraints weight = 6172.493| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 1.87 r_work: 0.3703 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4723 Z= 0.149 Angle : 0.647 11.151 6428 Z= 0.322 Chirality : 0.042 0.200 734 Planarity : 0.004 0.035 758 Dihedral : 11.666 155.980 854 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.89 % Allowed : 19.79 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.38), residues: 533 helix: 1.60 (0.29), residues: 332 sheet: -0.54 (1.25), residues: 17 loop : -0.46 (0.49), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 512 TYR 0.026 0.001 TYR A 519 PHE 0.025 0.002 PHE A 712 TRP 0.016 0.001 TRP A 505 HIS 0.004 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 4722) covalent geometry : angle 0.64705 ( 6426) SS BOND : bond 0.00045 ( 1) SS BOND : angle 0.93369 ( 2) hydrogen bonds : bond 0.04248 ( 263) hydrogen bonds : angle 4.54520 ( 747) ********************** 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: 14 poor density : 84 time to evaluate : 0.103 Fit side-chains revert: symmetry clash REVERT: A 31 THR cc_start: 0.9020 (m) cc_final: 0.8538 (p) REVERT: A 185 ASN cc_start: 0.6929 (t0) cc_final: 0.6515 (t0) REVERT: A 258 LYS cc_start: 0.8021 (tttt) cc_final: 0.7620 (tmmt) REVERT: A 402 LEU cc_start: 0.8965 (mp) cc_final: 0.8677 (mt) REVERT: A 414 ASP cc_start: 0.7337 (OUTLIER) cc_final: 0.6896 (p0) REVERT: A 571 ASN cc_start: 0.8099 (m-40) cc_final: 0.7790 (m110) REVERT: A 652 MET cc_start: 0.7161 (mmt) cc_final: 0.6829 (mmt) REVERT: A 654 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8636 (mm) REVERT: A 674 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.6723 (mmtp) outliers start: 14 outliers final: 9 residues processed: 92 average time/residue: 0.0425 time to fit residues: 5.3287 Evaluate side-chains 94 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.094 ------------------------------------------------------------------------------- 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 490 LEU Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 736 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 53 optimal weight: 0.0570 chunk 24 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 41 optimal weight: 0.0980 chunk 21 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 47 optimal weight: 0.1980 chunk 40 optimal weight: 0.6980 chunk 17 optimal weight: 0.2980 overall best weight: 0.2698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4192 r_free = 0.4192 target = 0.184909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.153881 restraints weight = 6172.940| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 1.88 r_work: 0.3760 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.5055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 4723 Z= 0.115 Angle : 0.590 10.773 6428 Z= 0.294 Chirality : 0.040 0.187 734 Planarity : 0.004 0.036 758 Dihedral : 11.129 153.358 854 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.06 % Allowed : 20.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.38), residues: 533 helix: 1.85 (0.29), residues: 335 sheet: -0.24 (1.30), residues: 17 loop : -0.49 (0.49), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 433 TYR 0.014 0.001 TYR A 519 PHE 0.029 0.001 PHE A 712 TRP 0.012 0.001 TRP A 407 HIS 0.004 0.001 HIS A 403 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 4722) covalent geometry : angle 0.59004 ( 6426) SS BOND : bond 0.00047 ( 1) SS BOND : angle 0.61388 ( 2) hydrogen bonds : bond 0.03805 ( 263) hydrogen bonds : angle 4.29064 ( 747) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1067.03 seconds wall clock time: 18 minutes 55.91 seconds (1135.91 seconds total)