Starting phenix.real_space_refine on Thu Jul 2 00:23:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wg3_37501/07_2026/8wg3_37501.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wg3_37501/07_2026/8wg3_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_37501/07_2026/8wg3_37501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wg3_37501/07_2026/8wg3_37501.map" model { file = "/net/cci-nas-00/data/ceres_data/8wg3_37501/07_2026/8wg3_37501.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wg3_37501/07_2026/8wg3_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 Unresolved non-hydrogen dihedrals: 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: 1.06, per 1000 atoms: 0.23 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: 0.29 Conformation dependent library (CDL) restraints added in 157.4 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: 0.12 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: 0.50 Time building geometry restraints manager: 0.42 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 - 2.10: 5524 2.10 - 4.20: 813 4.20 - 6.30: 83 6.30 - 8.40: 4 8.40 - 10.50: 2 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: 2803 35.42 - 70.84: 77 70.84 - 106.25: 3 106.25 - 141.67: 4 141.67 - 177.09: 2 Dihedral angle restraints: 2889 sinusoidal: 1279 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 2886 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: 34 0.222 - 0.278: 5 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: 759 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 756 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: 0.240 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.600 Find NCS groups from input model: 0.010 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 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= 0.594 Angle : 1.464 10.503 6428 Z= 0.963 Chirality : 0.084 0.278 734 Planarity : 0.012 0.118 759 Dihedral : 16.540 177.090 1844 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 are 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/Z covalent geometry : bond 0.00906 / 0.59 ( 4722) covalent geometry : angle 1.46399 / 0.96 ( 6426) SS BOND : bond 0.01219 / 0.64 ( 1) SS BOND : angle 1.72417 / 1.01 ( 2) hydrogen bonds : bond 0.19564 / 13.03 ( 263) hydrogen bonds : angle 8.84995 / 6.01 ( 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 : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.6915 (mm) REVERT: A 44 VAL cc_start: 0.8418 (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: 0.8322 (mm-40) cc_final: 0.8120 (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: 0.0662 time to fit residues: 10.8574 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 : 0.152 ------------------------------------------------------------------------------- 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... 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 = 0.4062 r_free = 0.4062 target = 0.172050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.138863 restraints weight = 6515.509| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.94 r_work: 0.3586 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4723 Z= 0.160 Angle : 0.747 8.956 6428 Z= 0.377 Chirality : 0.044 0.209 734 Planarity : 0.005 0.037 759 Dihedral : 14.010 175.274 871 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.15 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 are not related in a simple way. whole: 0.09 (0.36), residues: 533 helix: 0.64 (0.28), residues: 336 sheet: 0.94 (1.31), residues: 17 loop : -1.02 (0.48), 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 0.020 0.002 PHE A 154 TRP 0.023 0.002 TRP A 485 HIS 0.006 0.001 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 ( 4722) covalent geometry : angle 0.74703 / 0.38 ( 6426) SS BOND : bond 0.00089 / 0.05 ( 1) SS BOND : angle 0.33002 / 0.18 ( 2) hydrogen bonds : bond 0.05130 / 3.35 ( 263) hydrogen bonds : angle 5.42360 / 3.80 ( 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 122 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.9068 (m) cc_final: 0.8623 (p) REVERT: A 36 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7003 (mm) REVERT: A 53 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7527 (tm) REVERT: A 181 ASP cc_start: 0.8221 (m-30) cc_final: 0.7871 (t0) REVERT: A 184 GLU cc_start: 0.8248 (mm-30) cc_final: 0.8009 (mm-30) REVERT: A 261 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7629 (tp30) REVERT: A 446 PHE cc_start: 0.7464 (t80) cc_final: 0.7231 (t80) REVERT: A 628 MET cc_start: 0.7656 (mmm) cc_final: 0.7208 (mmm) REVERT: A 652 MET cc_start: 0.7359 (mmt) cc_final: 0.6893 (mmt) REVERT: A 674 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.6764 (mmtm) REVERT: A 720 THR cc_start: 0.8798 (m) cc_final: 0.8431 (p) outliers start: 16 outliers final: 6 residues processed: 116 average time/residue: 0.0567 time to fit residues: 8.6286 Evaluate side-chains 91 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.163 ------------------------------------------------------------------------------- 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: 6.9990 chunk 51 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 380 ASN A 438 ASN A 504 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.173285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.140092 restraints weight = 6402.186| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 1.94 r_work: 0.3608 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4723 Z= 0.138 Angle : 0.656 8.262 6428 Z= 0.332 Chirality : 0.041 0.193 734 Planarity : 0.004 0.037 759 Dihedral : 13.373 174.893 865 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.68 % Allowed : 16.49 % 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 are not related in a simple way. whole: 0.82 (0.37), residues: 533 helix: 1.26 (0.28), residues: 336 sheet: 0.31 (1.28), residues: 17 loop : -0.73 (0.48), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 512 TYR 0.012 0.001 TYR A 637 PHE 0.016 0.002 PHE A 154 TRP 0.017 0.002 TRP A 407 HIS 0.006 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 4722) covalent geometry : angle 0.65573 / 0.33 ( 6426) SS BOND : bond 0.00017 / 0.01 ( 1) SS BOND : angle 0.45463 / 0.24 ( 2) hydrogen bonds : bond 0.04746 / 3.11 ( 263) hydrogen bonds : angle 4.93187 / 3.44 ( 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 109 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.9022 (m) cc_final: 0.8536 (p) REVERT: A 53 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7316 (tm) REVERT: A 185 ASN cc_start: 0.7515 (t0) cc_final: 0.7144 (t0) REVERT: A 261 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7625 (tp30) REVERT: A 262 GLU cc_start: 0.8421 (tp30) cc_final: 0.7650 (tm-30) REVERT: A 414 ASP cc_start: 0.7500 (OUTLIER) cc_final: 0.7070 (p0) REVERT: A 446 PHE cc_start: 0.7516 (t80) cc_final: 0.7260 (t80) REVERT: A 501 PHE cc_start: 0.6796 (m-80) cc_final: 0.6274 (m-10) REVERT: A 534 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8773 (mp) REVERT: A 628 MET cc_start: 0.7883 (mmm) cc_final: 0.7089 (mmm) REVERT: A 652 MET cc_start: 0.7160 (mmt) cc_final: 0.6683 (mmt) REVERT: A 674 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.6443 (mmtp) outliers start: 13 outliers final: 7 residues processed: 104 average time/residue: 0.0473 time to fit residues: 6.5342 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 : 0.096 ------------------------------------------------------------------------------- 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 132 ILE Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 206 TRP Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 640 THR 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: 3.9990 chunk 27 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 571 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.173821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.140821 restraints weight = 6447.006| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 1.97 r_work: 0.3608 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 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 0.037 4723 Z= 0.135 Angle : 0.633 7.628 6428 Z= 0.320 Chirality : 0.041 0.190 734 Planarity : 0.004 0.035 759 Dihedral : 13.028 171.828 863 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.51 % Allowed : 16.29 % Favored : 80.21 % 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 are not related in a simple way. whole: 0.93 (0.37), residues: 533 helix: 1.40 (0.29), residues: 335 sheet: -0.15 (1.17), residues: 17 loop : -0.74 (0.48), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 512 TYR 0.011 0.001 TYR A 637 PHE 0.015 0.002 PHE A 52 TRP 0.014 0.002 TRP A 485 HIS 0.005 0.001 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 4722) covalent geometry : angle 0.63331 / 0.32 ( 6426) SS BOND : bond 0.00108 / 0.06 ( 1) SS BOND : angle 0.36381 / 0.19 ( 2) hydrogen bonds : bond 0.04485 / 2.92 ( 263) hydrogen bonds : angle 4.76257 / 3.31 ( 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 104 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.9020 (m) cc_final: 0.8416 (p) REVERT: A 53 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7369 (tm) REVERT: A 62 LEU cc_start: 0.6807 (mt) cc_final: 0.6544 (mt) REVERT: A 181 ASP cc_start: 0.8552 (t0) cc_final: 0.8320 (t0) REVERT: A 258 LYS cc_start: 0.8242 (tttt) cc_final: 0.7768 (tmmt) REVERT: A 261 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7549 (mm-30) REVERT: A 262 GLU cc_start: 0.8241 (tp30) cc_final: 0.7749 (tm-30) REVERT: A 402 LEU cc_start: 0.8646 (mp) cc_final: 0.8281 (mt) REVERT: A 414 ASP cc_start: 0.7487 (OUTLIER) cc_final: 0.7053 (p0) REVERT: A 421 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7442 (mp0) REVERT: A 446 PHE cc_start: 0.7460 (t80) cc_final: 0.7132 (t80) REVERT: A 470 LEU cc_start: 0.6849 (OUTLIER) cc_final: 0.6605 (mt) REVERT: A 490 LEU cc_start: 0.8980 (tt) cc_final: 0.8437 (mm) REVERT: A 500 PHE cc_start: 0.7658 (t80) cc_final: 0.7451 (t80) REVERT: A 501 PHE cc_start: 0.6788 (m-80) cc_final: 0.6277 (m-10) REVERT: A 652 MET cc_start: 0.7208 (mmt) cc_final: 0.6819 (mmt) REVERT: A 654 LEU cc_start: 0.9155 (mm) cc_final: 0.8780 (mm) REVERT: A 674 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.6260 (mmtp) outliers start: 17 outliers final: 8 residues processed: 101 average time/residue: 0.0459 time to fit residues: 6.2657 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 : 0.161 ------------------------------------------------------------------------------- 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 421 GLU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 523 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 1 optimal weight: 0.0970 chunk 5 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 17 optimal weight: 0.0060 chunk 44 optimal weight: 0.0370 overall best weight: 0.2872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 GLN A 504 HIS A 682 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.195805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.166748 restraints weight = 6371.645| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 1.80 r_work: 0.3940 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3836 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.4177 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= 0.111 Angle : 0.587 7.565 6428 Z= 0.294 Chirality : 0.040 0.198 734 Planarity : 0.004 0.036 759 Dihedral : 12.472 169.087 863 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.38), residues: 533 helix: 1.72 (0.29), residues: 335 sheet: -0.27 (1.17), residues: 17 loop : -0.52 (0.50), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 512 TYR 0.009 0.001 TYR A 637 PHE 0.018 0.001 PHE A 59 TRP 0.015 0.001 TRP A 407 HIS 0.009 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 ( 4722) covalent geometry : angle 0.58662 / 0.29 ( 6426) SS BOND : bond 0.00887 / 0.47 ( 1) SS BOND : angle 0.43810 / 0.24 ( 2) hydrogen bonds : bond 0.04061 / 2.65 ( 263) hydrogen bonds : angle 4.55420 / 3.15 ( 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 105 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8856 (m) cc_final: 0.8207 (p) REVERT: A 181 ASP cc_start: 0.8531 (t0) cc_final: 0.8184 (t0) REVERT: A 258 LYS cc_start: 0.8258 (tttt) cc_final: 0.7862 (tmmt) REVERT: A 262 GLU cc_start: 0.8378 (tp30) cc_final: 0.7973 (tm-30) REVERT: A 402 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8457 (mt) REVERT: A 414 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.7415 (p0) REVERT: A 490 LEU cc_start: 0.8547 (tt) cc_final: 0.8104 (mm) REVERT: A 501 PHE cc_start: 0.6666 (m-80) cc_final: 0.6412 (m-10) REVERT: A 652 MET cc_start: 0.6948 (mmt) cc_final: 0.6573 (mmt) REVERT: A 654 LEU cc_start: 0.8841 (mm) cc_final: 0.8439 (mm) REVERT: A 674 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.6504 (mmtp) outliers start: 14 outliers final: 7 residues processed: 100 average time/residue: 0.0517 time to fit residues: 6.9345 Evaluate side-chains 98 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.136 ------------------------------------------------------------------------------- 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 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 584 ASP 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 26 optimal weight: 0.0010 chunk 53 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 47 optimal weight: 0.0980 chunk 29 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 chunk 41 optimal weight: 0.0870 chunk 11 optimal weight: 0.6980 overall best weight: 0.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 571 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.196122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.166936 restraints weight = 6404.819| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 1.78 r_work: 0.3946 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3840 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.4384 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= 0.111 Angle : 0.587 8.196 6428 Z= 0.292 Chirality : 0.040 0.194 734 Planarity : 0.004 0.035 759 Dihedral : 12.197 164.494 861 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.27 % Allowed : 18.56 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.38), residues: 533 helix: 1.65 (0.29), residues: 340 sheet: -0.29 (1.18), residues: 17 loop : -0.56 (0.51), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 192 TYR 0.008 0.001 TYR A 637 PHE 0.014 0.001 PHE A 59 TRP 0.019 0.001 TRP A 407 HIS 0.005 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 ( 4722) covalent geometry : angle 0.58744 / 0.29 ( 6426) SS BOND : bond 0.00182 / 0.10 ( 1) SS BOND : angle 0.34309 / 0.18 ( 2) hydrogen bonds : bond 0.03994 / 2.59 ( 263) hydrogen bonds : angle 4.38642 / 3.02 ( 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 104 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8818 (m) cc_final: 0.8603 (m) REVERT: A 181 ASP cc_start: 0.8478 (t0) cc_final: 0.8083 (t0) REVERT: A 185 ASN cc_start: 0.7825 (t0) cc_final: 0.7365 (t0) REVERT: A 258 LYS cc_start: 0.8242 (tttt) cc_final: 0.7852 (tmmt) REVERT: A 262 GLU cc_start: 0.8290 (tp30) cc_final: 0.7946 (tm-30) REVERT: A 402 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8694 (mt) REVERT: A 490 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8265 (mm) REVERT: A 652 MET cc_start: 0.6941 (mmt) cc_final: 0.6589 (mmt) REVERT: A 654 LEU cc_start: 0.9083 (mm) cc_final: 0.8627 (mm) REVERT: A 674 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.6160 (mmtp) outliers start: 11 outliers final: 6 residues processed: 99 average time/residue: 0.0512 time to fit residues: 6.7938 Evaluate side-chains 95 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.160 ------------------------------------------------------------------------------- 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 490 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 19 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.193586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.163765 restraints weight = 6363.665| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 1.85 r_work: 0.3870 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3759 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4723 Z= 0.144 Angle : 0.630 9.144 6428 Z= 0.313 Chirality : 0.042 0.187 734 Planarity : 0.004 0.035 759 Dihedral : 12.349 162.687 861 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % 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 are not related in a simple way. whole: 1.15 (0.38), residues: 533 helix: 1.60 (0.29), residues: 334 sheet: -0.56 (1.20), residues: 17 loop : -0.63 (0.48), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 702 TYR 0.030 0.001 TYR A 519 PHE 0.018 0.002 PHE A 712 TRP 0.016 0.002 TRP A 505 HIS 0.004 0.001 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 4722) covalent geometry : angle 0.63006 / 0.31 ( 6426) SS BOND : bond 0.00114 / 0.06 ( 1) SS BOND : angle 0.41157 / 0.22 ( 2) hydrogen bonds : bond 0.04326 / 2.78 ( 263) hydrogen bonds : angle 4.51997 / 3.12 ( 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 98 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8998 (m) cc_final: 0.8346 (p) REVERT: A 185 ASN cc_start: 0.7758 (t0) cc_final: 0.7199 (t0) REVERT: A 186 ASN cc_start: 0.7022 (p0) cc_final: 0.6738 (p0) REVERT: A 258 LYS cc_start: 0.8215 (tttt) cc_final: 0.7783 (tmmt) REVERT: A 402 LEU cc_start: 0.8864 (mp) cc_final: 0.8626 (mt) REVERT: A 414 ASP cc_start: 0.7563 (OUTLIER) cc_final: 0.7180 (p0) REVERT: A 420 TRP cc_start: 0.7211 (OUTLIER) cc_final: 0.7003 (m-10) REVERT: A 652 MET cc_start: 0.7125 (mmt) cc_final: 0.6733 (mmt) REVERT: A 654 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8674 (mm) REVERT: A 674 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.6429 (mmtp) outliers start: 16 outliers final: 6 residues processed: 92 average time/residue: 0.0510 time to fit residues: 6.4270 Evaluate side-chains 93 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.135 ------------------------------------------------------------------------------- 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 420 TRP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 31 optimal weight: 0.0870 chunk 44 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 39 optimal weight: 0.0470 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 571 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.181891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.150606 restraints weight = 6270.009| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 1.88 r_work: 0.3723 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.4609 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= 0.122 Angle : 0.602 9.824 6428 Z= 0.298 Chirality : 0.040 0.195 734 Planarity : 0.004 0.035 759 Dihedral : 12.177 160.823 861 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.47 % Allowed : 20.00 % 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 are not related in a simple way. whole: 1.17 (0.38), residues: 533 helix: 1.58 (0.29), residues: 340 sheet: -0.40 (1.24), residues: 17 loop : -0.63 (0.49), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 192 TYR 0.030 0.001 TYR A 519 PHE 0.018 0.001 PHE A 712 TRP 0.014 0.001 TRP A 407 HIS 0.004 0.001 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 4722) covalent geometry : angle 0.60249 / 0.30 ( 6426) SS BOND : bond 0.00058 / 0.03 ( 1) SS BOND : angle 0.40078 / 0.21 ( 2) hydrogen bonds : bond 0.04097 / 2.64 ( 263) hydrogen bonds : angle 4.40924 / 3.04 ( 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 99 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ASN cc_start: 0.7860 (t0) cc_final: 0.7319 (t0) REVERT: A 258 LYS cc_start: 0.8107 (tttt) cc_final: 0.7700 (tmmt) REVERT: A 402 LEU cc_start: 0.9046 (mp) cc_final: 0.8749 (mt) REVERT: A 414 ASP cc_start: 0.7449 (OUTLIER) cc_final: 0.7032 (p0) REVERT: A 490 LEU cc_start: 0.8636 (tt) cc_final: 0.8412 (mm) REVERT: A 652 MET cc_start: 0.7143 (mmt) cc_final: 0.6789 (mmt) REVERT: A 654 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8643 (mm) REVERT: A 674 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.6112 (mmtp) outliers start: 12 outliers final: 6 residues processed: 96 average time/residue: 0.0491 time to fit residues: 6.3738 Evaluate side-chains 91 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 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 654 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 37 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.175764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.143907 restraints weight = 6202.981| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 1.86 r_work: 0.3653 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 4723 Z= 0.195 Angle : 0.693 10.963 6428 Z= 0.347 Chirality : 0.045 0.198 734 Planarity : 0.004 0.034 759 Dihedral : 12.482 159.671 861 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.47 % Allowed : 19.38 % 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 are not related in a simple way. whole: 0.76 (0.37), residues: 533 helix: 1.34 (0.29), residues: 330 sheet: -0.87 (1.24), residues: 17 loop : -0.81 (0.46), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 702 TYR 0.019 0.001 TYR A 519 PHE 0.023 0.002 PHE A 52 TRP 0.017 0.002 TRP A 505 HIS 0.004 0.001 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.19 ( 4722) covalent geometry : angle 0.69298 / 0.35 ( 6426) SS BOND : bond 0.00265 / 0.14 ( 1) SS BOND : angle 0.32933 / 0.18 ( 2) hydrogen bonds : bond 0.04785 / 3.07 ( 263) hydrogen bonds : angle 4.75526 / 3.28 ( 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 94 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.9126 (m) cc_final: 0.8735 (p) REVERT: A 185 ASN cc_start: 0.7314 (t0) cc_final: 0.6939 (t0) REVERT: A 258 LYS cc_start: 0.8145 (tttt) cc_final: 0.7730 (tmmt) REVERT: A 402 LEU cc_start: 0.8781 (mp) cc_final: 0.8520 (mt) REVERT: A 414 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.6984 (p0) REVERT: A 652 MET cc_start: 0.7187 (mmt) cc_final: 0.6831 (mmt) REVERT: A 654 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8661 (mm) REVERT: A 674 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.6446 (mmtp) outliers start: 12 outliers final: 8 residues processed: 89 average time/residue: 0.0494 time to fit residues: 5.9467 Evaluate side-chains 97 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.166 ------------------------------------------------------------------------------- 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 437 ILE 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 37 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 chunk 0 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 12 optimal weight: 0.1980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 406 ASN A 571 ASN ** A 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.181097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.149962 restraints weight = 6192.453| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 1.86 r_work: 0.3709 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3601 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4723 Z= 0.126 Angle : 0.614 11.048 6428 Z= 0.306 Chirality : 0.041 0.196 734 Planarity : 0.004 0.036 759 Dihedral : 12.097 157.495 861 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.47 % Allowed : 19.59 % 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 are not related in a simple way. whole: 1.07 (0.38), residues: 533 helix: 1.52 (0.29), residues: 338 sheet: -0.61 (1.28), residues: 17 loop : -0.69 (0.48), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 192 TYR 0.019 0.001 TYR A 519 PHE 0.018 0.001 PHE A 712 TRP 0.013 0.001 TRP A 407 HIS 0.004 0.001 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 4722) covalent geometry : angle 0.61426 / 0.31 ( 6426) SS BOND : bond 0.00060 / 0.03 ( 1) SS BOND : angle 0.38959 / 0.21 ( 2) hydrogen bonds : bond 0.04159 / 2.69 ( 263) hydrogen bonds : angle 4.45512 / 3.07 ( 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 102 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8962 (m) cc_final: 0.8559 (p) REVERT: A 185 ASN cc_start: 0.7577 (t0) cc_final: 0.7278 (t0) REVERT: A 258 LYS cc_start: 0.8018 (tttt) cc_final: 0.7609 (tmmt) REVERT: A 402 LEU cc_start: 0.8964 (mp) cc_final: 0.8689 (mt) REVERT: A 414 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.6943 (p0) REVERT: A 652 MET cc_start: 0.7130 (mmt) cc_final: 0.6768 (mmt) REVERT: A 654 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8646 (mm) REVERT: A 674 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.6680 (mmtp) outliers start: 12 outliers final: 7 residues processed: 98 average time/residue: 0.0460 time to fit residues: 6.1982 Evaluate side-chains 98 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.159 ------------------------------------------------------------------------------- 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 437 ILE 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 53 optimal weight: 0.0970 chunk 24 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 33 optimal weight: 0.0670 chunk 41 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 47 optimal weight: 0.0570 chunk 40 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.3634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4190 r_free = 0.4190 target = 0.184279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.153813 restraints weight = 6180.937| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 1.77 r_work: 0.3720 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4723 Z= 0.118 Angle : 0.597 11.001 6428 Z= 0.299 Chirality : 0.040 0.199 734 Planarity : 0.004 0.036 759 Dihedral : 11.477 151.445 861 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.44 % Allowed : 20.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.38), residues: 533 helix: 1.71 (0.29), residues: 339 sheet: -0.40 (1.28), residues: 17 loop : -0.61 (0.48), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 660 TYR 0.029 0.001 TYR A 519 PHE 0.018 0.001 PHE A 712 TRP 0.011 0.001 TRP A 407 HIS 0.003 0.001 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 ( 4722) covalent geometry : angle 0.59663 / 0.30 ( 6426) SS BOND : bond 0.00067 / 0.04 ( 1) SS BOND : angle 0.33226 / 0.18 ( 2) hydrogen bonds : bond 0.03957 / 2.55 ( 263) hydrogen bonds : angle 4.30541 / 2.97 ( 747) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1093.59 seconds wall clock time: 19 minutes 24.29 seconds (1164.29 seconds total)