Starting phenix.real_space_refine on Wed Sep 17 08:21:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xca_38238/09_2025/8xca_38238_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xca_38238/09_2025/8xca_38238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xca_38238/09_2025/8xca_38238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xca_38238/09_2025/8xca_38238.map" model { file = "/net/cci-nas-00/data/ceres_data/8xca_38238/09_2025/8xca_38238_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xca_38238/09_2025/8xca_38238_neut.cif" } resolution = 3.1 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= 0.000 sd= 0.008 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 79 5.49 5 S 23 5.16 5 C 4179 2.51 5 N 1306 2.21 5 O 1519 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7106 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5443 Classifications: {'peptide': 668} Link IDs: {'PTRANS': 21, 'TRANS': 646} Chain breaks: 4 Chain: "B" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1066 Classifications: {'RNA': 50} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 2, 'rna3p_pur': 21, 'rna3p_pyr': 22} Link IDs: {'rna2p': 6, 'rna3p': 43} Chain: "C" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 431 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "D" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 166 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Time building chain proxies: 1.95, per 1000 atoms: 0.27 Number of scatterers: 7106 At special positions: 0 Unit cell: (81.84, 96.36, 111.54, 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 23 16.00 P 79 15.00 O 1519 8.00 N 1306 7.00 C 4179 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: 0.66 Conformation dependent library (CDL) restraints added in 394.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1264 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 8 sheets defined 45.5% alpha, 16.0% beta 32 base pairs and 52 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 15 through 41 removed outlier: 3.599A pdb=" N ARG A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 69 Processing helix chain 'A' and resid 76 through 88 Processing helix chain 'A' and resid 100 through 103 Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 187 through 199 Processing helix chain 'A' and resid 211 through 240 removed outlier: 3.620A pdb=" N CYS A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 459 Processing helix chain 'A' and resid 522 through 553 removed outlier: 3.553A pdb=" N ASP A 551 " --> pdb=" O LYS A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 566 Processing helix chain 'A' and resid 566 through 572 Processing helix chain 'A' and resid 578 through 607 removed outlier: 3.730A pdb=" N ARG A 583 " --> pdb=" O ALA A 579 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 609 No H-bonds generated for 'chain 'A' and resid 608 through 609' Processing helix chain 'A' and resid 610 through 614 removed outlier: 4.478A pdb=" N ASP A 614 " --> pdb=" O SER A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 642 removed outlier: 3.772A pdb=" N ARG A 642 " --> pdb=" O LYS A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 689 removed outlier: 3.509A pdb=" N HIS A 689 " --> pdb=" O THR A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 719 Processing helix chain 'A' and resid 721 through 736 removed outlier: 3.965A pdb=" N VAL A 725 " --> pdb=" O ALA A 721 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU A 726 " --> pdb=" O PRO A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 796 removed outlier: 3.590A pdb=" N ALA A 786 " --> pdb=" O ALA A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 829 removed outlier: 3.500A pdb=" N ARG A 824 " --> pdb=" O ARG A 820 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 11 removed outlier: 4.400A pdb=" N TYR A 433 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASP A 438 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLU A 423 " --> pdb=" O ASP A 438 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 56 removed outlier: 4.111A pdb=" N TYR A 44 " --> pdb=" O VAL A 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 360 through 365 Processing sheet with id=AA4, first strand: chain 'A' and resid 391 through 397 removed outlier: 5.437A pdb=" N ASN A 392 " --> pdb=" O THR A 408 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N THR A 408 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 514 through 517 removed outlier: 5.743A pdb=" N LEU A 479 " --> pdb=" O GLU A 697 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL A 694 " --> pdb=" O TRP A 741 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL A 743 " --> pdb=" O VAL A 694 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N MET A 696 " --> pdb=" O VAL A 743 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 499 through 501 removed outlier: 4.176A pdb=" N ILE A 499 " --> pdb=" O PHE A 511 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 760 through 761 Processing sheet with id=AA8, first strand: chain 'A' and resid 806 through 810 removed outlier: 3.846A pdb=" N LEU A 809 " --> pdb=" O ARG A 813 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ARG A 813 " --> pdb=" O LEU A 809 " (cutoff:3.500A) 287 hydrogen bonds defined for protein. 822 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 52 stacking parallelities Total time for adding SS restraints: 1.69 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1743 1.33 - 1.45: 1820 1.45 - 1.57: 3650 1.57 - 1.69: 155 1.69 - 1.81: 35 Bond restraints: 7403 Sorted by residual: bond pdb=" CG ARG A 615 " pdb=" CD ARG A 615 " ideal model delta sigma weight residual 1.520 1.570 -0.050 3.00e-02 1.11e+03 2.82e+00 bond pdb=" CA ASP A 658 " pdb=" CB ASP A 658 " ideal model delta sigma weight residual 1.532 1.556 -0.025 1.82e-02 3.02e+03 1.86e+00 bond pdb=" C ASN A 482 " pdb=" N PRO A 483 " ideal model delta sigma weight residual 1.333 1.346 -0.013 1.20e-02 6.94e+03 1.09e+00 bond pdb=" CB ASP A 756 " pdb=" CG ASP A 756 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 8.88e-01 bond pdb=" O3' A B -21 " pdb=" P G B -20 " ideal model delta sigma weight residual 1.607 1.621 -0.014 1.50e-02 4.44e+03 8.20e-01 ... (remaining 7398 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 10145 1.65 - 3.29: 166 3.29 - 4.94: 22 4.94 - 6.58: 7 6.58 - 8.23: 3 Bond angle restraints: 10343 Sorted by residual: angle pdb=" CB ARG A 615 " pdb=" CG ARG A 615 " pdb=" CD ARG A 615 " ideal model delta sigma weight residual 111.30 119.53 -8.23 2.30e+00 1.89e-01 1.28e+01 angle pdb=" CG ARG A 615 " pdb=" CD ARG A 615 " pdb=" NE ARG A 615 " ideal model delta sigma weight residual 112.00 118.36 -6.36 2.20e+00 2.07e-01 8.36e+00 angle pdb=" C ASP A 658 " pdb=" CA ASP A 658 " pdb=" CB ASP A 658 " ideal model delta sigma weight residual 109.71 114.55 -4.84 1.83e+00 2.99e-01 7.00e+00 angle pdb=" CB MET A 219 " pdb=" CG MET A 219 " pdb=" SD MET A 219 " ideal model delta sigma weight residual 112.70 120.23 -7.53 3.00e+00 1.11e-01 6.31e+00 angle pdb=" CA GLU A 730 " pdb=" CB GLU A 730 " pdb=" CG GLU A 730 " ideal model delta sigma weight residual 114.10 119.04 -4.94 2.00e+00 2.50e-01 6.10e+00 ... (remaining 10338 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 4111 35.80 - 71.60: 351 71.60 - 107.40: 19 107.40 - 143.21: 1 143.21 - 179.01: 1 Dihedral angle restraints: 4483 sinusoidal: 2529 harmonic: 1954 Sorted by residual: dihedral pdb=" O4' U B -32 " pdb=" C1' U B -32 " pdb=" N1 U B -32 " pdb=" C2 U B -32 " ideal model delta sinusoidal sigma weight residual -128.00 51.01 -179.01 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA ASN A 482 " pdb=" C ASN A 482 " pdb=" N PRO A 483 " pdb=" CA PRO A 483 " ideal model delta harmonic sigma weight residual 180.00 155.51 24.49 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" O4' A B -21 " pdb=" C1' A B -21 " pdb=" N9 A B -21 " pdb=" C4 A B -21 " ideal model delta sinusoidal sigma weight residual 70.00 -1.31 71.31 1 2.00e+01 2.50e-03 1.63e+01 ... (remaining 4480 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 875 0.032 - 0.064: 209 0.064 - 0.097: 62 0.097 - 0.129: 23 0.129 - 0.161: 4 Chirality restraints: 1173 Sorted by residual: chirality pdb=" C1' A B -7 " pdb=" O4' A B -7 " pdb=" C2' A B -7 " pdb=" N9 A B -7 " both_signs ideal model delta sigma weight residual False 2.46 2.30 0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" P G B -20 " pdb=" OP1 G B -20 " pdb=" OP2 G B -20 " pdb=" O5' G B -20 " both_signs ideal model delta sigma weight residual True 2.41 -2.57 -0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" CA VAL A 427 " pdb=" N VAL A 427 " pdb=" C VAL A 427 " pdb=" CB VAL A 427 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.01e-01 ... (remaining 1170 not shown) Planarity restraints: 1048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 11 " 0.024 2.00e-02 2.50e+03 1.08e-02 3.48e+00 pdb=" N9 G B 11 " -0.027 2.00e-02 2.50e+03 pdb=" C8 G B 11 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G B 11 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G B 11 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G B 11 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G B 11 " 0.008 2.00e-02 2.50e+03 pdb=" N1 G B 11 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G B 11 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G B 11 " -0.000 2.00e-02 2.50e+03 pdb=" N3 G B 11 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G B 11 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 12 " 0.021 2.00e-02 2.50e+03 1.03e-02 2.91e+00 pdb=" N9 A B 12 " -0.026 2.00e-02 2.50e+03 pdb=" C8 A B 12 " 0.000 2.00e-02 2.50e+03 pdb=" N7 A B 12 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A B 12 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A B 12 " 0.001 2.00e-02 2.50e+03 pdb=" N6 A B 12 " 0.005 2.00e-02 2.50e+03 pdb=" N1 A B 12 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A B 12 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A B 12 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A B 12 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 658 " 0.008 2.00e-02 2.50e+03 1.58e-02 2.50e+00 pdb=" C ASP A 658 " -0.027 2.00e-02 2.50e+03 pdb=" O ASP A 658 " 0.010 2.00e-02 2.50e+03 pdb=" N GLU A 659 " 0.009 2.00e-02 2.50e+03 ... (remaining 1045 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 826 2.75 - 3.29: 6611 3.29 - 3.82: 12760 3.82 - 4.36: 14435 4.36 - 4.90: 23172 Nonbonded interactions: 57804 Sorted by model distance: nonbonded pdb=" OD2 ASP A 614 " pdb=" NH1 ARG A 615 " model vdw 2.212 3.120 nonbonded pdb=" OH TYR A 666 " pdb=" OP2 U B -32 " model vdw 2.225 3.040 nonbonded pdb=" OG SER A 106 " pdb=" OP2 DA D -3 " model vdw 2.251 3.040 nonbonded pdb=" NH2 ARG A 671 " pdb=" OP2 DG C -7 " model vdw 2.261 3.120 nonbonded pdb=" OG SER A 533 " pdb=" OD1 ASN A 632 " model vdw 2.280 3.040 ... (remaining 57799 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: 0.00 ========== 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: 4.630 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: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.610 Find NCS groups from input model: 0.030 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 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 : 0.002 0.050 7403 Z= 0.118 Angle : 0.535 8.227 10343 Z= 0.286 Chirality : 0.035 0.161 1173 Planarity : 0.003 0.031 1048 Dihedral : 21.671 179.008 3219 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.17 % Allowed : 26.07 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.33), residues: 658 helix: 2.48 (0.30), residues: 274 sheet: -0.03 (0.46), residues: 131 loop : -0.81 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 775 TYR 0.010 0.001 TYR A 605 PHE 0.010 0.001 PHE A 202 TRP 0.012 0.001 TRP A 645 HIS 0.002 0.000 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 7403) covalent geometry : angle 0.53485 (10343) hydrogen bonds : bond 0.14549 ( 368) hydrogen bonds : angle 5.07243 ( 976) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.155 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 36 average time/residue: 0.0984 time to fit residues: 4.9169 Evaluate side-chains 33 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 778 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.078048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.060018 restraints weight = 19728.783| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.86 r_work: 0.2828 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.0756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7403 Z= 0.198 Angle : 0.549 6.788 10343 Z= 0.294 Chirality : 0.037 0.156 1173 Planarity : 0.004 0.046 1048 Dihedral : 21.332 178.910 1859 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.92 % Allowed : 23.16 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.33), residues: 658 helix: 2.55 (0.30), residues: 279 sheet: 0.01 (0.48), residues: 109 loop : -0.73 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 561 TYR 0.014 0.001 TYR A 538 PHE 0.009 0.001 PHE A 537 TRP 0.007 0.001 TRP A 645 HIS 0.003 0.001 HIS A 609 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 7403) covalent geometry : angle 0.54919 (10343) hydrogen bonds : bond 0.04645 ( 368) hydrogen bonds : angle 4.03651 ( 976) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 35 time to evaluate : 0.241 Fit side-chains REVERT: A 202 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.7834 (t80) outliers start: 17 outliers final: 11 residues processed: 48 average time/residue: 0.0896 time to fit residues: 5.9503 Evaluate side-chains 43 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 816 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 18 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 46 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.077660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.059540 restraints weight = 19786.710| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.85 r_work: 0.2802 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 7403 Z= 0.222 Angle : 0.555 6.188 10343 Z= 0.296 Chirality : 0.037 0.162 1173 Planarity : 0.004 0.036 1048 Dihedral : 21.331 178.688 1859 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.46 % Allowed : 24.19 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.33), residues: 658 helix: 2.55 (0.29), residues: 279 sheet: -0.01 (0.48), residues: 109 loop : -0.70 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 527 TYR 0.014 0.001 TYR A 538 PHE 0.007 0.001 PHE A 771 TRP 0.005 0.001 TRP A 645 HIS 0.004 0.001 HIS A 609 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 7403) covalent geometry : angle 0.55488 (10343) hydrogen bonds : bond 0.04582 ( 368) hydrogen bonds : angle 3.84303 ( 976) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 33 time to evaluate : 0.252 Fit side-chains REVERT: A 202 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.7951 (t80) REVERT: A 626 MET cc_start: 0.9193 (tpt) cc_final: 0.8809 (tpt) outliers start: 26 outliers final: 14 residues processed: 54 average time/residue: 0.0874 time to fit residues: 6.5366 Evaluate side-chains 44 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 29 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 816 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 53 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 0.5980 chunk 55 optimal weight: 0.0770 chunk 16 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 41 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 overall best weight: 1.4742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.078310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.060120 restraints weight = 19938.189| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.86 r_work: 0.2808 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7403 Z= 0.169 Angle : 0.521 6.013 10343 Z= 0.280 Chirality : 0.036 0.146 1173 Planarity : 0.004 0.036 1048 Dihedral : 21.326 178.541 1859 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.26 % Allowed : 23.84 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.33), residues: 658 helix: 2.62 (0.29), residues: 279 sheet: 0.05 (0.48), residues: 109 loop : -0.68 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 746 TYR 0.010 0.001 TYR A 538 PHE 0.008 0.001 PHE A 202 TRP 0.005 0.001 TRP A 645 HIS 0.003 0.001 HIS A 609 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 7403) covalent geometry : angle 0.52126 (10343) hydrogen bonds : bond 0.04236 ( 368) hydrogen bonds : angle 3.72798 ( 976) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 32 time to evaluate : 0.236 Fit side-chains REVERT: A 202 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.7919 (t80) REVERT: A 544 ARG cc_start: 0.8672 (mtm180) cc_final: 0.8450 (mtm-85) REVERT: A 547 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8132 (mttt) outliers start: 19 outliers final: 13 residues processed: 46 average time/residue: 0.0956 time to fit residues: 5.9536 Evaluate side-chains 44 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 29 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 547 LYS Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 798 TYR Chi-restraints excluded: chain A residue 816 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 44 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 59 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.076998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.058946 restraints weight = 19860.366| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.88 r_work: 0.2777 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 7403 Z= 0.257 Angle : 0.571 5.988 10343 Z= 0.305 Chirality : 0.038 0.169 1173 Planarity : 0.004 0.037 1048 Dihedral : 21.391 178.962 1859 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.80 % Allowed : 23.16 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.33), residues: 658 helix: 2.57 (0.30), residues: 279 sheet: 0.03 (0.48), residues: 109 loop : -0.72 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 615 TYR 0.012 0.001 TYR A 538 PHE 0.009 0.001 PHE A 202 TRP 0.003 0.001 TRP A 720 HIS 0.004 0.001 HIS A 609 Details of bonding type rmsd covalent geometry : bond 0.00559 ( 7403) covalent geometry : angle 0.57108 (10343) hydrogen bonds : bond 0.04613 ( 368) hydrogen bonds : angle 3.79713 ( 976) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 31 time to evaluate : 0.240 Fit side-chains REVERT: A 202 PHE cc_start: 0.8648 (OUTLIER) cc_final: 0.7980 (t80) REVERT: A 805 TRP cc_start: 0.6580 (OUTLIER) cc_final: 0.5895 (m-10) outliers start: 28 outliers final: 19 residues processed: 54 average time/residue: 0.0985 time to fit residues: 7.1807 Evaluate side-chains 50 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 29 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 547 LYS Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 798 TYR Chi-restraints excluded: chain A residue 805 TRP Chi-restraints excluded: chain A residue 816 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.078499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.060432 restraints weight = 19879.923| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.87 r_work: 0.2822 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7403 Z= 0.135 Angle : 0.512 5.632 10343 Z= 0.276 Chirality : 0.035 0.154 1173 Planarity : 0.004 0.037 1048 Dihedral : 21.372 178.364 1859 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.12 % Allowed : 23.33 % Favored : 72.56 % 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 aren not related in a simple way. whole: 1.29 (0.33), residues: 658 helix: 2.62 (0.30), residues: 281 sheet: 0.10 (0.48), residues: 109 loop : -0.76 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 81 TYR 0.011 0.001 TYR A 605 PHE 0.011 0.001 PHE A 202 TRP 0.008 0.001 TRP A 640 HIS 0.003 0.001 HIS A 609 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 7403) covalent geometry : angle 0.51163 (10343) hydrogen bonds : bond 0.04106 ( 368) hydrogen bonds : angle 3.65328 ( 976) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 32 time to evaluate : 0.165 Fit side-chains REVERT: A 202 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.7898 (t80) REVERT: A 547 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8102 (mttt) outliers start: 24 outliers final: 16 residues processed: 51 average time/residue: 0.0830 time to fit residues: 5.9356 Evaluate side-chains 47 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 29 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 547 LYS Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 798 TYR Chi-restraints excluded: chain A residue 816 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 57 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.076440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.058472 restraints weight = 19889.588| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.85 r_work: 0.2781 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 7403 Z= 0.260 Angle : 0.578 6.031 10343 Z= 0.308 Chirality : 0.038 0.169 1173 Planarity : 0.004 0.037 1048 Dihedral : 21.434 179.074 1859 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.46 % Allowed : 23.16 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.33), residues: 658 helix: 2.55 (0.30), residues: 279 sheet: 0.11 (0.48), residues: 109 loop : -0.69 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 81 TYR 0.014 0.001 TYR A 798 PHE 0.009 0.001 PHE A 202 TRP 0.003 0.001 TRP A 805 HIS 0.004 0.001 HIS A 26 Details of bonding type rmsd covalent geometry : bond 0.00567 ( 7403) covalent geometry : angle 0.57811 (10343) hydrogen bonds : bond 0.04595 ( 368) hydrogen bonds : angle 3.77873 ( 976) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 31 time to evaluate : 0.256 Fit side-chains REVERT: A 202 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.7996 (t80) REVERT: A 458 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8159 (ptm160) REVERT: A 615 ARG cc_start: 0.8680 (mmm160) cc_final: 0.8347 (mmm160) REVERT: A 805 TRP cc_start: 0.6563 (OUTLIER) cc_final: 0.5888 (m-10) REVERT: A 828 GLU cc_start: 0.5774 (OUTLIER) cc_final: 0.4278 (mm-30) outliers start: 26 outliers final: 19 residues processed: 53 average time/residue: 0.1095 time to fit residues: 7.4812 Evaluate side-chains 52 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 29 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 547 LYS Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 798 TYR Chi-restraints excluded: chain A residue 805 TRP Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 828 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 16 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 42 optimal weight: 0.0470 chunk 66 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.078548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.060530 restraints weight = 19737.812| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.86 r_work: 0.2827 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7403 Z= 0.133 Angle : 0.512 5.506 10343 Z= 0.276 Chirality : 0.035 0.157 1173 Planarity : 0.004 0.035 1048 Dihedral : 21.402 178.068 1859 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.77 % Allowed : 22.98 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.33), residues: 658 helix: 2.60 (0.30), residues: 281 sheet: 0.19 (0.48), residues: 109 loop : -0.74 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 40 TYR 0.011 0.001 TYR A 605 PHE 0.011 0.001 PHE A 202 TRP 0.009 0.001 TRP A 640 HIS 0.003 0.001 HIS A 609 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 7403) covalent geometry : angle 0.51202 (10343) hydrogen bonds : bond 0.04016 ( 368) hydrogen bonds : angle 3.64690 ( 976) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 35 time to evaluate : 0.148 Fit side-chains REVERT: A 202 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.7883 (t80) REVERT: A 828 GLU cc_start: 0.5674 (OUTLIER) cc_final: 0.4168 (mm-30) outliers start: 22 outliers final: 15 residues processed: 53 average time/residue: 0.0999 time to fit residues: 7.0125 Evaluate side-chains 49 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 32 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 547 LYS Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 798 TYR Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 828 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 55 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.079453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.061427 restraints weight = 19812.408| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.88 r_work: 0.2849 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7403 Z= 0.122 Angle : 0.515 5.997 10343 Z= 0.275 Chirality : 0.035 0.155 1173 Planarity : 0.003 0.033 1048 Dihedral : 21.347 178.702 1859 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.43 % Allowed : 23.67 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.33), residues: 658 helix: 2.59 (0.30), residues: 281 sheet: 0.19 (0.48), residues: 109 loop : -0.74 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 615 TYR 0.011 0.001 TYR A 605 PHE 0.012 0.001 PHE A 202 TRP 0.008 0.001 TRP A 645 HIS 0.002 0.000 HIS A 609 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 7403) covalent geometry : angle 0.51480 (10343) hydrogen bonds : bond 0.03841 ( 368) hydrogen bonds : angle 3.59225 ( 976) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 36 time to evaluate : 0.244 Fit side-chains REVERT: A 202 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.7812 (t80) REVERT: A 481 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8701 (mt) REVERT: A 828 GLU cc_start: 0.5618 (OUTLIER) cc_final: 0.4057 (mm-30) outliers start: 20 outliers final: 14 residues processed: 51 average time/residue: 0.0812 time to fit residues: 5.7467 Evaluate side-chains 51 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 34 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 547 LYS Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 798 TYR Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 828 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 55 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.076119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.058128 restraints weight = 20035.867| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.90 r_work: 0.2764 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 7403 Z= 0.346 Angle : 0.665 10.659 10343 Z= 0.351 Chirality : 0.040 0.188 1173 Planarity : 0.005 0.041 1048 Dihedral : 21.508 178.971 1859 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.26 % Allowed : 23.84 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.33), residues: 658 helix: 2.41 (0.30), residues: 283 sheet: 0.05 (0.48), residues: 109 loop : -0.70 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 625 TYR 0.016 0.002 TYR A 798 PHE 0.011 0.002 PHE A 794 TRP 0.007 0.001 TRP A 640 HIS 0.004 0.001 HIS A 26 Details of bonding type rmsd covalent geometry : bond 0.00755 ( 7403) covalent geometry : angle 0.66499 (10343) hydrogen bonds : bond 0.05015 ( 368) hydrogen bonds : angle 3.89527 ( 976) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 30 time to evaluate : 0.238 Fit side-chains REVERT: A 202 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.8127 (t80) REVERT: A 805 TRP cc_start: 0.6599 (OUTLIER) cc_final: 0.5911 (m-10) REVERT: A 828 GLU cc_start: 0.5904 (OUTLIER) cc_final: 0.4532 (mm-30) outliers start: 19 outliers final: 16 residues processed: 45 average time/residue: 0.0870 time to fit residues: 5.4478 Evaluate side-chains 44 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 25 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 547 LYS Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 798 TYR Chi-restraints excluded: chain A residue 805 TRP Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 828 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 13 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 24 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.077645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.059616 restraints weight = 19804.907| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.85 r_work: 0.2812 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7403 Z= 0.151 Angle : 0.554 8.779 10343 Z= 0.296 Chirality : 0.036 0.160 1173 Planarity : 0.004 0.035 1048 Dihedral : 21.505 178.516 1859 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.09 % Allowed : 24.36 % Favored : 72.56 % 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 aren not related in a simple way. whole: 1.27 (0.33), residues: 658 helix: 2.49 (0.30), residues: 283 sheet: 0.07 (0.48), residues: 109 loop : -0.65 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 615 TYR 0.011 0.001 TYR A 605 PHE 0.011 0.001 PHE A 202 TRP 0.007 0.001 TRP A 640 HIS 0.003 0.001 HIS A 609 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 7403) covalent geometry : angle 0.55427 (10343) hydrogen bonds : bond 0.04202 ( 368) hydrogen bonds : angle 3.73878 ( 976) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1513.97 seconds wall clock time: 26 minutes 49.22 seconds (1609.22 seconds total)