Starting phenix.real_space_refine on Tue May 13 00:04:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u53_41911/05_2025/8u53_41911.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u53_41911/05_2025/8u53_41911.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u53_41911/05_2025/8u53_41911.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u53_41911/05_2025/8u53_41911.map" model { file = "/net/cci-nas-00/data/ceres_data/8u53_41911/05_2025/8u53_41911.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u53_41911/05_2025/8u53_41911.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 4 5.49 5 S 34 5.16 5 C 6476 2.51 5 N 1442 2.21 5 O 1606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9562 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1439 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain breaks: 1 Chain: "A" Number of atoms: 3078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3078 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 16, 'TRANS': 378} Chain breaks: 4 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'UNK:plan-1': 37} Unresolved non-hydrogen planarities: 37 Chain: "B" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1439 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain breaks: 1 Chain: "B" Number of atoms: 3078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3078 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 16, 'TRANS': 378} Chain breaks: 4 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'UNK:plan-1': 37} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 264 Unusual residues: {'82T': 1, 'CPL': 1, 'PLM': 10} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 264 Unusual residues: {'82T': 1, 'CPL': 1, 'PLM': 10} Classifications: {'undetermined': 12} Link IDs: {None: 11} Time building chain proxies: 5.94, per 1000 atoms: 0.62 Number of scatterers: 9562 At special positions: 0 Unit cell: (130.81, 118.45, 90.64, 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 34 16.00 P 4 15.00 O 1606 8.00 N 1442 7.00 C 6476 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 1.0 seconds 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2192 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 2 sheets defined 84.6% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 2 through 28 Processing helix chain 'A' and resid 29 through 32 removed outlier: 6.543A pdb=" N GLY A 32 " --> pdb=" O ARG A 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 29 through 32' Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 38 through 44 Processing helix chain 'A' and resid 59 through 67 Processing helix chain 'A' and resid 69 through 78 Processing helix chain 'A' and resid 78 through 102 removed outlier: 3.529A pdb=" N LEU A 101 " --> pdb=" O CYS A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 184 Processing helix chain 'A' and resid 188 through 191 Processing helix chain 'A' and resid 207 through 220 Processing helix chain 'A' and resid 235 through 246 Processing helix chain 'A' and resid 281 through 303 Processing helix chain 'A' and resid 317 through 325 Processing helix chain 'A' and resid 343 through 347 Processing helix chain 'A' and resid 348 through 352 Processing helix chain 'A' and resid 355 through 377 Processing helix chain 'A' and resid 377 through 388 Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 416 through 427 Processing helix chain 'A' and resid 428 through 439 removed outlier: 3.503A pdb=" N LEU A 432 " --> pdb=" O MET A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 463 Processing helix chain 'A' and resid 464 through 474 Processing helix chain 'A' and resid 490 through 498 Processing helix chain 'A' and resid 501 through 523 removed outlier: 3.841A pdb=" N TYR A 517 " --> pdb=" O PHE A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 537 Processing helix chain 'A' and resid 540 through 549 removed outlier: 3.591A pdb=" N TRP A 548 " --> pdb=" O VAL A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 573 Proline residue: A 560 - end of helix Processing helix chain 'A' and resid 578 through 601 Processing helix chain 'A' and resid 612 through 638 Processing helix chain 'A' and resid 642 through 645 Processing helix chain 'A' and resid 646 through 665 Processing helix chain 'A' and resid 666 through 669 Processing helix chain 'A' and resid 672 through 677 Processing helix chain 'A' and resid 685 through 692 Processing helix chain 'B' and resid 3 through 28 Processing helix chain 'B' and resid 29 through 32 removed outlier: 6.543A pdb=" N GLY B 32 " --> pdb=" O ARG B 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 29 through 32' Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 38 through 44 Processing helix chain 'B' and resid 59 through 67 Processing helix chain 'B' and resid 69 through 78 Processing helix chain 'B' and resid 78 through 102 removed outlier: 3.529A pdb=" N LEU B 101 " --> pdb=" O CYS B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 184 Processing helix chain 'B' and resid 188 through 191 Processing helix chain 'B' and resid 207 through 220 Processing helix chain 'B' and resid 235 through 246 Processing helix chain 'B' and resid 281 through 303 Processing helix chain 'B' and resid 317 through 325 Processing helix chain 'B' and resid 343 through 347 Processing helix chain 'B' and resid 348 through 352 Processing helix chain 'B' and resid 355 through 377 Processing helix chain 'B' and resid 377 through 388 Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 416 through 427 Processing helix chain 'B' and resid 428 through 439 removed outlier: 3.504A pdb=" N LEU B 432 " --> pdb=" O MET B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 463 Processing helix chain 'B' and resid 464 through 474 Processing helix chain 'B' and resid 490 through 498 Processing helix chain 'B' and resid 501 through 523 removed outlier: 3.841A pdb=" N TYR B 517 " --> pdb=" O PHE B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 537 Processing helix chain 'B' and resid 540 through 549 removed outlier: 3.591A pdb=" N TRP B 548 " --> pdb=" O VAL B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 573 Proline residue: B 560 - end of helix Processing helix chain 'B' and resid 578 through 601 Processing helix chain 'B' and resid 612 through 638 Processing helix chain 'B' and resid 642 through 645 Processing helix chain 'B' and resid 646 through 665 Processing helix chain 'B' and resid 666 through 669 Processing helix chain 'B' and resid 672 through 677 Processing helix chain 'B' and resid 685 through 692 Processing sheet with id=AA1, first strand: chain 'A' and resid 226 through 229 removed outlier: 3.530A pdb=" N ARG A 226 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 226 through 229 removed outlier: 3.531A pdb=" N ARG B 226 " --> pdb=" O PHE B 314 " (cutoff:3.500A) 655 hydrogen bonds defined for protein. 1911 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: 2.92 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1587 1.31 - 1.44: 3076 1.44 - 1.58: 4940 1.58 - 1.71: 121 1.71 - 1.84: 60 Bond restraints: 9784 Sorted by residual: bond pdb=" O4P CPL A 801 " pdb=" P CPL A 801 " ideal model delta sigma weight residual 1.648 1.798 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" O4P CPL B 802 " pdb=" P CPL B 802 " ideal model delta sigma weight residual 1.648 1.798 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" C10 82T B 803 " pdb=" C9 82T B 803 " ideal model delta sigma weight residual 1.524 1.379 0.145 2.00e-02 2.50e+03 5.28e+01 bond pdb=" C10 82T A 802 " pdb=" C9 82T A 802 " ideal model delta sigma weight residual 1.524 1.379 0.145 2.00e-02 2.50e+03 5.27e+01 bond pdb=" CB LEU B 566 " pdb=" CG LEU B 566 " ideal model delta sigma weight residual 1.530 1.397 0.133 2.00e-02 2.50e+03 4.40e+01 ... (remaining 9779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.28: 12324 3.28 - 6.56: 773 6.56 - 9.84: 49 9.84 - 13.13: 6 13.13 - 16.41: 4 Bond angle restraints: 13156 Sorted by residual: angle pdb=" N VAL B 601 " pdb=" CA VAL B 601 " pdb=" C VAL B 601 " ideal model delta sigma weight residual 111.62 118.85 -7.23 7.90e-01 1.60e+00 8.38e+01 angle pdb=" N VAL A 601 " pdb=" CA VAL A 601 " pdb=" C VAL A 601 " ideal model delta sigma weight residual 111.62 118.82 -7.20 7.90e-01 1.60e+00 8.31e+01 angle pdb=" C ALA A 576 " pdb=" N PRO A 577 " pdb=" CA PRO A 577 " ideal model delta sigma weight residual 119.56 128.78 -9.22 1.02e+00 9.61e-01 8.17e+01 angle pdb=" C ALA B 576 " pdb=" N PRO B 577 " pdb=" CA PRO B 577 " ideal model delta sigma weight residual 119.56 128.76 -9.20 1.02e+00 9.61e-01 8.14e+01 angle pdb=" CA PHE A 513 " pdb=" CB PHE A 513 " pdb=" CG PHE A 513 " ideal model delta sigma weight residual 113.80 122.41 -8.61 1.00e+00 1.00e+00 7.41e+01 ... (remaining 13151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.85: 5670 34.85 - 69.70: 120 69.70 - 104.56: 16 104.56 - 139.41: 4 139.41 - 174.26: 6 Dihedral angle restraints: 5816 sinusoidal: 2434 harmonic: 3382 Sorted by residual: dihedral pdb=" C3 CPL B 802 " pdb=" C1 CPL B 802 " pdb=" C2 CPL B 802 " pdb=" O3P CPL B 802 " ideal model delta sinusoidal sigma weight residual 72.09 -102.17 174.26 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 CPL A 801 " pdb=" C1 CPL A 801 " pdb=" C2 CPL A 801 " pdb=" O3P CPL A 801 " ideal model delta sinusoidal sigma weight residual 72.09 -102.17 174.26 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O2 CPL A 801 " pdb=" C1 CPL A 801 " pdb=" C2 CPL A 801 " pdb=" O3P CPL A 801 " ideal model delta sinusoidal sigma weight residual 309.18 135.88 173.30 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 5813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 1076 0.106 - 0.212: 319 0.212 - 0.318: 61 0.318 - 0.424: 6 0.424 - 0.530: 6 Chirality restraints: 1468 Sorted by residual: chirality pdb=" C2 CPL A 801 " pdb=" C1 CPL A 801 " pdb=" C3 CPL A 801 " pdb=" O2 CPL A 801 " both_signs ideal model delta sigma weight residual False -2.32 -2.85 0.53 2.00e-01 2.50e+01 7.01e+00 chirality pdb=" C2 CPL B 802 " pdb=" C1 CPL B 802 " pdb=" C3 CPL B 802 " pdb=" O2 CPL B 802 " both_signs ideal model delta sigma weight residual False -2.32 -2.84 0.53 2.00e-01 2.50e+01 6.96e+00 chirality pdb=" CG LEU A 102 " pdb=" CB LEU A 102 " pdb=" CD1 LEU A 102 " pdb=" CD2 LEU A 102 " both_signs ideal model delta sigma weight residual False -2.59 -3.07 0.48 2.00e-01 2.50e+01 5.73e+00 ... (remaining 1465 not shown) Planarity restraints: 1572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 171 " -0.068 2.00e-02 2.50e+03 3.46e-02 2.39e+01 pdb=" CG TYR A 171 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR A 171 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR A 171 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR A 171 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 171 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 171 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 171 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 171 " 0.068 2.00e-02 2.50e+03 3.44e-02 2.37e+01 pdb=" CG TYR B 171 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR B 171 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR B 171 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR B 171 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B 171 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR B 171 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR B 171 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 215 " 0.045 2.00e-02 2.50e+03 2.72e-02 1.48e+01 pdb=" CG TYR B 215 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR B 215 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR B 215 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR B 215 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR B 215 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR B 215 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR B 215 " 0.048 2.00e-02 2.50e+03 ... (remaining 1569 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 4899 2.98 - 3.46: 9897 3.46 - 3.94: 15885 3.94 - 4.42: 20207 4.42 - 4.90: 29622 Nonbonded interactions: 80510 Sorted by model distance: nonbonded pdb=" NH1 ARG A 178 " pdb=" O GLY A 667 " model vdw 2.498 3.120 nonbonded pdb=" NH1 ARG B 178 " pdb=" O GLY B 667 " model vdw 2.499 3.120 nonbonded pdb=" C SER A 501 " pdb=" OG SER A 501 " model vdw 2.534 2.616 nonbonded pdb=" C SER B 501 " pdb=" OG SER B 501 " model vdw 2.534 2.616 nonbonded pdb=" CB PLM A 809 " pdb=" CE PLM A 809 " model vdw 2.553 3.072 ... (remaining 80505 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 231 or resid 234 through 697 or resid 804 throug \ h 812)) selection = (chain 'B' and (resid 2 through 231 or resid 234 through 697 or resid 804 throug \ h 812)) } 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: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.910 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 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 : 0.024 0.150 9784 Z= 1.271 Angle : 1.715 16.408 13156 Z= 1.115 Chirality : 0.104 0.530 1468 Planarity : 0.009 0.036 1572 Dihedral : 15.246 174.260 3624 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 0.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.24), residues: 1054 helix: 0.53 (0.17), residues: 742 sheet: None (None), residues: 0 loop : 0.70 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.009 TRP A 336 HIS 0.006 0.002 HIS A 696 PHE 0.037 0.007 PHE A 513 TYR 0.068 0.009 TYR A 171 ARG 0.008 0.001 ARG A 359 Details of bonding type rmsd hydrogen bonds : bond 0.14151 ( 655) hydrogen bonds : angle 6.72633 ( 1911) covalent geometry : bond 0.02432 ( 9784) covalent geometry : angle 1.71491 (13156) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 343 GLU cc_start: 0.7298 (tt0) cc_final: 0.7037 (tt0) REVERT: B 343 GLU cc_start: 0.7362 (tt0) cc_final: 0.7078 (tt0) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 1.0699 time to fit residues: 207.6605 Evaluate side-chains 121 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.135322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.113183 restraints weight = 14242.910| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.86 r_work: 0.3493 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9784 Z= 0.165 Angle : 0.605 9.013 13156 Z= 0.327 Chirality : 0.043 0.164 1468 Planarity : 0.005 0.042 1572 Dihedral : 17.474 177.878 1666 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.90 % Allowed : 6.45 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.25), residues: 1054 helix: 1.42 (0.18), residues: 760 sheet: None (None), residues: 0 loop : 0.45 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 613 HIS 0.005 0.002 HIS A 696 PHE 0.037 0.003 PHE B 513 TYR 0.019 0.002 TYR B 536 ARG 0.004 0.001 ARG A 178 Details of bonding type rmsd hydrogen bonds : bond 0.04914 ( 655) hydrogen bonds : angle 5.20766 ( 1911) covalent geometry : bond 0.00366 ( 9784) covalent geometry : angle 0.60495 (13156) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.947 Fit side-chains REVERT: A 428 MET cc_start: 0.6815 (OUTLIER) cc_final: 0.5919 (tmt) REVERT: A 431 LYS cc_start: 0.7099 (tmtt) cc_final: 0.6851 (tttm) REVERT: A 579 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7843 (pp) REVERT: B 428 MET cc_start: 0.6812 (OUTLIER) cc_final: 0.5997 (tmt) REVERT: B 431 LYS cc_start: 0.7127 (tmtt) cc_final: 0.6873 (tttm) REVERT: B 579 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7865 (pp) outliers start: 27 outliers final: 8 residues processed: 166 average time/residue: 0.9548 time to fit residues: 172.4096 Evaluate side-chains 125 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 694 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 40.0000 chunk 99 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.133793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.112130 restraints weight = 14376.803| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.85 r_work: 0.3462 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9784 Z= 0.166 Angle : 0.583 7.280 13156 Z= 0.311 Chirality : 0.042 0.164 1468 Planarity : 0.005 0.035 1572 Dihedral : 16.480 175.063 1666 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.01 % Allowed : 10.22 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.25), residues: 1054 helix: 1.48 (0.18), residues: 760 sheet: None (None), residues: 0 loop : 0.11 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 613 HIS 0.005 0.001 HIS A 447 PHE 0.029 0.002 PHE B 513 TYR 0.015 0.002 TYR B 171 ARG 0.008 0.001 ARG A 56 Details of bonding type rmsd hydrogen bonds : bond 0.04667 ( 655) hydrogen bonds : angle 5.01843 ( 1911) covalent geometry : bond 0.00378 ( 9784) covalent geometry : angle 0.58293 (13156) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 1.103 Fit side-chains REVERT: A 332 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8578 (mtp) REVERT: A 431 LYS cc_start: 0.7199 (OUTLIER) cc_final: 0.6948 (tttm) REVERT: A 579 ILE cc_start: 0.8353 (tt) cc_final: 0.7829 (pp) REVERT: B 431 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6960 (tttm) REVERT: B 579 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.7840 (pp) outliers start: 28 outliers final: 16 residues processed: 153 average time/residue: 0.8597 time to fit residues: 145.0114 Evaluate side-chains 137 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 694 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 74 optimal weight: 30.0000 chunk 95 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.134194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.112649 restraints weight = 14292.054| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.84 r_work: 0.3472 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9784 Z= 0.142 Angle : 0.529 6.455 13156 Z= 0.283 Chirality : 0.041 0.156 1468 Planarity : 0.004 0.036 1572 Dihedral : 16.056 173.509 1666 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.69 % Allowed : 11.08 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.26), residues: 1054 helix: 1.50 (0.18), residues: 762 sheet: None (None), residues: 0 loop : 0.08 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 613 HIS 0.004 0.001 HIS A 447 PHE 0.028 0.002 PHE A 513 TYR 0.016 0.001 TYR B 157 ARG 0.005 0.000 ARG A 56 Details of bonding type rmsd hydrogen bonds : bond 0.04255 ( 655) hydrogen bonds : angle 4.87496 ( 1911) covalent geometry : bond 0.00318 ( 9784) covalent geometry : angle 0.52907 (13156) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 1.103 Fit side-chains REVERT: A 76 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8534 (tp) REVERT: A 332 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8556 (mtp) REVERT: A 428 MET cc_start: 0.6755 (OUTLIER) cc_final: 0.5915 (tmt) REVERT: A 431 LYS cc_start: 0.7202 (OUTLIER) cc_final: 0.6955 (tttm) REVERT: A 579 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.7817 (pp) REVERT: B 76 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8549 (tp) REVERT: B 431 LYS cc_start: 0.7208 (OUTLIER) cc_final: 0.6967 (tttm) REVERT: B 579 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.7825 (pp) outliers start: 25 outliers final: 12 residues processed: 140 average time/residue: 0.8297 time to fit residues: 128.2420 Evaluate side-chains 135 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 694 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 55 optimal weight: 0.9990 chunk 17 optimal weight: 20.0000 chunk 53 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 85 optimal weight: 0.4980 chunk 24 optimal weight: 0.2980 chunk 43 optimal weight: 0.9990 chunk 28 optimal weight: 0.2980 chunk 103 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.135864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.114647 restraints weight = 14261.263| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.84 r_work: 0.3502 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9784 Z= 0.118 Angle : 0.498 6.807 13156 Z= 0.265 Chirality : 0.039 0.148 1468 Planarity : 0.004 0.030 1572 Dihedral : 15.602 172.375 1666 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.80 % Allowed : 12.15 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.26), residues: 1054 helix: 1.77 (0.19), residues: 752 sheet: None (None), residues: 0 loop : 0.20 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 548 HIS 0.002 0.001 HIS B 447 PHE 0.025 0.002 PHE B 513 TYR 0.014 0.001 TYR B 157 ARG 0.006 0.000 ARG B 56 Details of bonding type rmsd hydrogen bonds : bond 0.03872 ( 655) hydrogen bonds : angle 4.73332 ( 1911) covalent geometry : bond 0.00252 ( 9784) covalent geometry : angle 0.49830 (13156) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 1.002 Fit side-chains REVERT: A 76 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8491 (tp) REVERT: A 161 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7701 (mm) REVERT: A 428 MET cc_start: 0.6893 (OUTLIER) cc_final: 0.6053 (tmt) REVERT: A 431 LYS cc_start: 0.7169 (OUTLIER) cc_final: 0.6951 (tttm) REVERT: A 579 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.7779 (pp) REVERT: B 71 GLN cc_start: 0.8606 (tp40) cc_final: 0.8364 (mm-40) REVERT: B 76 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8489 (tp) REVERT: B 428 MET cc_start: 0.6785 (OUTLIER) cc_final: 0.5940 (tmt) REVERT: B 431 LYS cc_start: 0.7178 (OUTLIER) cc_final: 0.6954 (tttm) REVERT: B 579 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.7778 (pp) outliers start: 26 outliers final: 8 residues processed: 131 average time/residue: 0.8832 time to fit residues: 127.1431 Evaluate side-chains 135 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 584 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 38 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 73 optimal weight: 20.0000 chunk 86 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 28 optimal weight: 0.0470 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.133300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.111713 restraints weight = 14374.854| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.85 r_work: 0.3459 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9784 Z= 0.153 Angle : 0.539 7.103 13156 Z= 0.286 Chirality : 0.041 0.160 1468 Planarity : 0.004 0.032 1572 Dihedral : 15.685 171.459 1666 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.37 % Allowed : 13.01 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.25), residues: 1054 helix: 1.60 (0.18), residues: 762 sheet: None (None), residues: 0 loop : -0.02 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 613 HIS 0.005 0.001 HIS A 447 PHE 0.028 0.002 PHE A 513 TYR 0.010 0.001 TYR A 157 ARG 0.004 0.000 ARG B 56 Details of bonding type rmsd hydrogen bonds : bond 0.04176 ( 655) hydrogen bonds : angle 4.76308 ( 1911) covalent geometry : bond 0.00352 ( 9784) covalent geometry : angle 0.53890 (13156) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.932 Fit side-chains REVERT: A 76 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8543 (tp) REVERT: A 222 GLU cc_start: 0.6664 (mp0) cc_final: 0.6346 (tt0) REVERT: A 428 MET cc_start: 0.6913 (OUTLIER) cc_final: 0.6073 (tmt) REVERT: A 431 LYS cc_start: 0.7163 (tmtt) cc_final: 0.6903 (tttm) REVERT: A 594 LEU cc_start: 0.8496 (mt) cc_final: 0.8291 (mm) REVERT: B 76 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8551 (tp) REVERT: B 222 GLU cc_start: 0.6642 (mp0) cc_final: 0.6316 (tt0) REVERT: B 428 MET cc_start: 0.6885 (OUTLIER) cc_final: 0.6047 (tmt) REVERT: B 431 LYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6918 (tttm) REVERT: B 579 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.7840 (pp) REVERT: B 594 LEU cc_start: 0.8503 (mt) cc_final: 0.8296 (mm) outliers start: 22 outliers final: 6 residues processed: 139 average time/residue: 0.9494 time to fit residues: 143.5889 Evaluate side-chains 133 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 579 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 17 optimal weight: 20.0000 chunk 110 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 41 optimal weight: 0.0870 chunk 46 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.131340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.109396 restraints weight = 14438.942| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.86 r_work: 0.3424 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9784 Z= 0.185 Angle : 0.579 7.800 13156 Z= 0.308 Chirality : 0.043 0.163 1468 Planarity : 0.005 0.035 1572 Dihedral : 15.992 169.840 1666 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.26 % Allowed : 13.44 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.25), residues: 1054 helix: 1.36 (0.18), residues: 762 sheet: None (None), residues: 0 loop : -0.18 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 613 HIS 0.006 0.002 HIS A 447 PHE 0.031 0.002 PHE B 513 TYR 0.017 0.002 TYR A 225 ARG 0.004 0.000 ARG B 450 Details of bonding type rmsd hydrogen bonds : bond 0.04487 ( 655) hydrogen bonds : angle 4.85904 ( 1911) covalent geometry : bond 0.00433 ( 9784) covalent geometry : angle 0.57897 (13156) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.999 Fit side-chains REVERT: A 428 MET cc_start: 0.6902 (OUTLIER) cc_final: 0.6051 (tmt) REVERT: A 431 LYS cc_start: 0.7281 (OUTLIER) cc_final: 0.7017 (tttm) REVERT: A 594 LEU cc_start: 0.8572 (mt) cc_final: 0.8339 (mm) REVERT: B 198 ASP cc_start: 0.8652 (m-30) cc_final: 0.8420 (m-30) REVERT: B 428 MET cc_start: 0.6889 (OUTLIER) cc_final: 0.6041 (tmt) REVERT: B 431 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.7048 (tttm) REVERT: B 594 LEU cc_start: 0.8580 (mt) cc_final: 0.8346 (mm) outliers start: 21 outliers final: 10 residues processed: 134 average time/residue: 0.9344 time to fit residues: 137.5898 Evaluate side-chains 131 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 431 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 60 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 17 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.133419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.111668 restraints weight = 14630.921| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.88 r_work: 0.3463 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9784 Z= 0.132 Angle : 0.526 8.102 13156 Z= 0.280 Chirality : 0.040 0.150 1468 Planarity : 0.004 0.034 1572 Dihedral : 15.720 169.791 1666 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.47 % Allowed : 13.66 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.26), residues: 1054 helix: 1.57 (0.18), residues: 760 sheet: None (None), residues: 0 loop : -0.14 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 548 HIS 0.004 0.001 HIS B 696 PHE 0.027 0.002 PHE A 513 TYR 0.020 0.001 TYR B 225 ARG 0.003 0.000 ARG B 56 Details of bonding type rmsd hydrogen bonds : bond 0.04019 ( 655) hydrogen bonds : angle 4.70104 ( 1911) covalent geometry : bond 0.00293 ( 9784) covalent geometry : angle 0.52576 (13156) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.945 Fit side-chains REVERT: A 428 MET cc_start: 0.6912 (OUTLIER) cc_final: 0.6063 (tmt) REVERT: A 431 LYS cc_start: 0.7215 (OUTLIER) cc_final: 0.6968 (tttm) REVERT: B 428 MET cc_start: 0.6877 (OUTLIER) cc_final: 0.6031 (tmt) REVERT: B 431 LYS cc_start: 0.7250 (OUTLIER) cc_final: 0.7010 (tttm) outliers start: 23 outliers final: 8 residues processed: 138 average time/residue: 0.9229 time to fit residues: 139.1710 Evaluate side-chains 130 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 694 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 88 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 16 optimal weight: 0.3980 chunk 90 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.134328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.112889 restraints weight = 14478.089| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.85 r_work: 0.3470 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9784 Z= 0.132 Angle : 0.531 8.205 13156 Z= 0.281 Chirality : 0.040 0.152 1468 Planarity : 0.004 0.033 1572 Dihedral : 15.723 169.125 1666 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.15 % Allowed : 14.84 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.26), residues: 1054 helix: 1.71 (0.18), residues: 748 sheet: None (None), residues: 0 loop : 0.01 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 613 HIS 0.004 0.001 HIS B 696 PHE 0.026 0.002 PHE B 513 TYR 0.022 0.001 TYR A 225 ARG 0.003 0.000 ARG B 56 Details of bonding type rmsd hydrogen bonds : bond 0.03954 ( 655) hydrogen bonds : angle 4.68052 ( 1911) covalent geometry : bond 0.00293 ( 9784) covalent geometry : angle 0.53136 (13156) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.920 Fit side-chains REVERT: A 414 GLU cc_start: 0.7718 (pt0) cc_final: 0.7513 (pp20) REVERT: A 428 MET cc_start: 0.6891 (OUTLIER) cc_final: 0.6043 (tmt) REVERT: A 431 LYS cc_start: 0.7185 (OUTLIER) cc_final: 0.6932 (tttm) REVERT: B 428 MET cc_start: 0.6780 (OUTLIER) cc_final: 0.5921 (tmt) REVERT: B 431 LYS cc_start: 0.7184 (OUTLIER) cc_final: 0.6929 (tttm) outliers start: 20 outliers final: 9 residues processed: 132 average time/residue: 0.9427 time to fit residues: 135.9774 Evaluate side-chains 135 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 694 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 91 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 75 optimal weight: 40.0000 chunk 74 optimal weight: 20.0000 chunk 68 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 41 optimal weight: 0.4980 chunk 83 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.132200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.110623 restraints weight = 14514.054| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.85 r_work: 0.3434 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9784 Z= 0.174 Angle : 0.575 8.351 13156 Z= 0.306 Chirality : 0.042 0.162 1468 Planarity : 0.005 0.035 1572 Dihedral : 15.976 167.876 1666 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.72 % Allowed : 15.38 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.26), residues: 1054 helix: 1.44 (0.18), residues: 760 sheet: None (None), residues: 0 loop : -0.21 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 613 HIS 0.006 0.002 HIS B 447 PHE 0.030 0.002 PHE B 513 TYR 0.016 0.002 TYR B 225 ARG 0.004 0.000 ARG A 450 Details of bonding type rmsd hydrogen bonds : bond 0.04293 ( 655) hydrogen bonds : angle 4.79719 ( 1911) covalent geometry : bond 0.00404 ( 9784) covalent geometry : angle 0.57547 (13156) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 1.027 Fit side-chains REVERT: A 428 MET cc_start: 0.6827 (OUTLIER) cc_final: 0.5957 (tmt) REVERT: A 431 LYS cc_start: 0.7190 (OUTLIER) cc_final: 0.6908 (tttm) REVERT: B 428 MET cc_start: 0.6831 (OUTLIER) cc_final: 0.5970 (tmt) REVERT: B 431 LYS cc_start: 0.7257 (OUTLIER) cc_final: 0.6970 (tttm) outliers start: 16 outliers final: 7 residues processed: 125 average time/residue: 0.8882 time to fit residues: 122.2061 Evaluate side-chains 130 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 431 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 15 optimal weight: 0.0670 chunk 102 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 18 optimal weight: 30.0000 chunk 29 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.133820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.112457 restraints weight = 14609.647| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.85 r_work: 0.3461 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9784 Z= 0.138 Angle : 0.539 8.461 13156 Z= 0.285 Chirality : 0.041 0.153 1468 Planarity : 0.004 0.034 1572 Dihedral : 15.803 167.932 1666 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.51 % Allowed : 15.70 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.26), residues: 1054 helix: 1.57 (0.18), residues: 764 sheet: None (None), residues: 0 loop : -0.07 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 613 HIS 0.004 0.001 HIS A 696 PHE 0.027 0.002 PHE A 513 TYR 0.011 0.001 TYR B 157 ARG 0.002 0.000 ARG B 56 Details of bonding type rmsd hydrogen bonds : bond 0.03990 ( 655) hydrogen bonds : angle 4.69040 ( 1911) covalent geometry : bond 0.00314 ( 9784) covalent geometry : angle 0.53856 (13156) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7188.99 seconds wall clock time: 124 minutes 24.81 seconds (7464.81 seconds total)