Starting phenix.real_space_refine on Tue Jan 14 18:10:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xca_38238/01_2025/8xca_38238_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xca_38238/01_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_38238/01_2025/8xca_38238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xca_38238/01_2025/8xca_38238.map" model { file = "/net/cci-nas-00/data/ceres_data/8xca_38238/01_2025/8xca_38238_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xca_38238/01_2025/8xca_38238_neut.cif" } resolution = 3.1 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= 0.008 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 5.81, per 1000 atoms: 0.82 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: 2.01 Conformation dependent library (CDL) restraints added in 651.6 milliseconds 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: 2.51 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: 3.13 Time building geometry restraints manager: 2.23 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: 3.660 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.330 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.280 ------------------------------------------------------------------------------- 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= 0.146 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 (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: 1.11 (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 TRP 0.012 0.001 TRP A 645 HIS 0.002 0.000 HIS A 526 PHE 0.010 0.001 PHE A 202 TYR 0.010 0.001 TYR A 605 ARG 0.002 0.000 ARG A 775 *********************** 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 : 0.829 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 36 average time/residue: 0.2195 time to fit residues: 11.1200 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 : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 18 optimal weight: 0.4980 chunk 37 optimal weight: 7.9990 chunk 29 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- 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 = 0.3409 r_free = 0.3409 target = 0.079930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.061965 restraints weight = 19289.057| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.84 r_work: 0.2856 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.0684 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= 0.190 Angle : 0.522 6.765 10343 Z= 0.281 Chirality : 0.035 0.159 1173 Planarity : 0.004 0.045 1048 Dihedral : 21.304 178.718 1859 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.57 % Allowed : 23.50 % 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 (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: 1.24 (0.33), residues: 658 helix: 2.56 (0.30), residues: 279 sheet: 0.06 (0.48), residues: 109 loop : -0.72 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 645 HIS 0.002 0.001 HIS A 609 PHE 0.010 0.001 PHE A 537 TYR 0.013 0.001 TYR A 538 ARG 0.008 0.000 ARG A 561 *********************** 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 51 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 36 time to evaluate : 0.709 Fit side-chains REVERT: A 202 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7763 (t80) REVERT: A 219 MET cc_start: 0.9048 (tpp) cc_final: 0.8730 (tpp) REVERT: A 481 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8683 (mt) outliers start: 15 outliers final: 9 residues processed: 47 average time/residue: 0.2016 time to fit residues: 13.2593 Evaluate side-chains 43 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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 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 52 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 59 optimal weight: 0.3980 chunk 64 optimal weight: 0.2980 chunk 36 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3418 r_free = 0.3418 target = 0.080032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.061977 restraints weight = 19578.950| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.86 r_work: 0.2868 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7403 Z= 0.145 Angle : 0.488 6.510 10343 Z= 0.263 Chirality : 0.034 0.158 1173 Planarity : 0.003 0.031 1048 Dihedral : 21.203 177.899 1859 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.12 % Allowed : 22.81 % Favored : 73.07 % 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: 1.30 (0.33), residues: 658 helix: 2.59 (0.30), residues: 281 sheet: 0.15 (0.48), residues: 109 loop : -0.73 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 645 HIS 0.001 0.000 HIS A 609 PHE 0.009 0.001 PHE A 537 TYR 0.010 0.001 TYR A 538 ARG 0.003 0.000 ARG A 775 *********************** 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 63 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 39 time to evaluate : 0.680 Fit side-chains REVERT: A 202 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7729 (t80) REVERT: A 481 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8722 (mt) REVERT: A 547 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8067 (mttt) outliers start: 24 outliers final: 8 residues processed: 59 average time/residue: 0.2419 time to fit residues: 18.8969 Evaluate side-chains 47 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 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 547 LYS Chi-restraints excluded: chain A residue 763 LEU 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 1 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 0.0070 chunk 7 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.078460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.060308 restraints weight = 19956.571| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.90 r_work: 0.2814 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1132 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= 0.297 Angle : 0.544 7.093 10343 Z= 0.288 Chirality : 0.036 0.148 1173 Planarity : 0.004 0.034 1048 Dihedral : 21.234 178.891 1859 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.60 % Allowed : 24.19 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.33 (0.33), residues: 658 helix: 2.65 (0.30), residues: 281 sheet: 0.12 (0.47), residues: 109 loop : -0.74 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 720 HIS 0.004 0.001 HIS A 26 PHE 0.008 0.001 PHE A 32 TYR 0.012 0.001 TYR A 538 ARG 0.004 0.000 ARG A 775 *********************** 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 57 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 36 time to evaluate : 0.661 Fit side-chains REVERT: A 202 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.7938 (t80) REVERT: A 547 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8093 (mttt) outliers start: 21 outliers final: 13 residues processed: 51 average time/residue: 0.2373 time to fit residues: 16.2067 Evaluate side-chains 47 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 32 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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 547 LYS Chi-restraints excluded: chain A residue 589 THR 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 816 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 54 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 13 optimal weight: 0.0970 chunk 61 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 overall best weight: 0.8178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.079447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.061320 restraints weight = 19686.493| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.88 r_work: 0.2856 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7403 Z= 0.164 Angle : 0.504 6.578 10343 Z= 0.269 Chirality : 0.035 0.147 1173 Planarity : 0.003 0.032 1048 Dihedral : 21.237 178.239 1859 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.11 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.33), residues: 658 helix: 2.72 (0.30), residues: 281 sheet: 0.15 (0.47), residues: 109 loop : -0.70 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 645 HIS 0.002 0.000 HIS A 26 PHE 0.008 0.001 PHE A 202 TYR 0.010 0.001 TYR A 22 ARG 0.005 0.000 ARG A 615 *********************** 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 57 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 38 time to evaluate : 0.684 Fit side-chains REVERT: A 202 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.7818 (t80) REVERT: A 481 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8682 (mt) outliers start: 19 outliers final: 13 residues processed: 52 average time/residue: 0.2893 time to fit residues: 19.7030 Evaluate side-chains 48 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 33 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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 65 LEU 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 547 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 72 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 28 optimal weight: 0.0370 chunk 48 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 overall best weight: 1.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.079013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.061033 restraints weight = 19747.543| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.86 r_work: 0.2846 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7403 Z= 0.196 Angle : 0.504 6.016 10343 Z= 0.269 Chirality : 0.035 0.148 1173 Planarity : 0.003 0.032 1048 Dihedral : 21.237 178.745 1859 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.43 % Allowed : 23.84 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.33), residues: 658 helix: 2.74 (0.30), residues: 281 sheet: 0.17 (0.48), residues: 109 loop : -0.72 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 645 HIS 0.003 0.001 HIS A 26 PHE 0.008 0.001 PHE A 202 TYR 0.010 0.001 TYR A 22 ARG 0.004 0.000 ARG A 775 *********************** 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 55 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 35 time to evaluate : 0.690 Fit side-chains REVERT: A 202 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.7870 (t80) outliers start: 20 outliers final: 12 residues processed: 50 average time/residue: 0.2017 time to fit residues: 14.0324 Evaluate side-chains 46 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 33 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 65 LEU Chi-restraints excluded: chain A residue 70 CYS 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 501 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 60 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.077149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.059174 restraints weight = 19798.184| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.87 r_work: 0.2794 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 7403 Z= 0.358 Angle : 0.587 8.601 10343 Z= 0.310 Chirality : 0.038 0.164 1173 Planarity : 0.004 0.033 1048 Dihedral : 21.364 178.970 1859 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.26 % Allowed : 24.87 % Favored : 71.87 % 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: 1.31 (0.33), residues: 658 helix: 2.62 (0.30), residues: 279 sheet: 0.05 (0.48), residues: 109 loop : -0.67 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 640 HIS 0.004 0.001 HIS A 26 PHE 0.010 0.001 PHE A 771 TYR 0.014 0.002 TYR A 798 ARG 0.003 0.000 ARG A 775 *********************** 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 53 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 34 time to evaluate : 0.723 Fit side-chains REVERT: A 202 PHE cc_start: 0.8685 (OUTLIER) cc_final: 0.8060 (t80) REVERT: A 828 GLU cc_start: 0.5673 (OUTLIER) cc_final: 0.4156 (mm-30) outliers start: 19 outliers final: 15 residues processed: 48 average time/residue: 0.2381 time to fit residues: 15.3994 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 : 0.718 ------------------------------------------------------------------------------- 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 65 LEU Chi-restraints excluded: chain A residue 70 CYS 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 501 SER Chi-restraints excluded: chain A residue 547 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 15 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 9 optimal weight: 0.1980 chunk 10 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.078582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.060357 restraints weight = 19572.319| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.87 r_work: 0.2832 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7403 Z= 0.181 Angle : 0.531 7.806 10343 Z= 0.280 Chirality : 0.035 0.147 1173 Planarity : 0.003 0.034 1048 Dihedral : 21.353 178.477 1859 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.26 % Allowed : 24.87 % Favored : 71.87 % 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: 1.33 (0.33), residues: 658 helix: 2.65 (0.30), residues: 281 sheet: 0.12 (0.48), residues: 109 loop : -0.73 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 640 HIS 0.003 0.001 HIS A 609 PHE 0.009 0.001 PHE A 202 TYR 0.010 0.001 TYR A 22 ARG 0.008 0.000 ARG A 615 *********************** 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 56 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 37 time to evaluate : 0.728 Fit side-chains REVERT: A 202 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.7948 (t80) REVERT: A 828 GLU cc_start: 0.5567 (OUTLIER) cc_final: 0.4030 (mm-30) outliers start: 19 outliers final: 13 residues processed: 52 average time/residue: 0.2267 time to fit residues: 15.9997 Evaluate side-chains 50 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 35 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 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 547 LYS Chi-restraints excluded: chain A residue 589 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 57 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 46 optimal weight: 0.1980 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.078720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.060677 restraints weight = 19789.044| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.89 r_work: 0.2837 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7403 Z= 0.195 Angle : 0.530 8.379 10343 Z= 0.282 Chirality : 0.035 0.145 1173 Planarity : 0.004 0.033 1048 Dihedral : 21.331 178.889 1859 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.09 % Allowed : 24.87 % 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 (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: 1.39 (0.33), residues: 658 helix: 2.67 (0.30), residues: 279 sheet: 0.14 (0.48), residues: 109 loop : -0.64 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 645 HIS 0.003 0.001 HIS A 609 PHE 0.009 0.001 PHE A 202 TYR 0.010 0.001 TYR A 538 ARG 0.006 0.000 ARG A 615 *********************** 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 54 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 36 time to evaluate : 0.741 Fit side-chains REVERT: A 202 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.7935 (t80) REVERT: A 481 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8741 (mt) REVERT: A 547 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8005 (mttt) REVERT: A 828 GLU cc_start: 0.5596 (OUTLIER) cc_final: 0.4036 (mm-30) outliers start: 18 outliers final: 14 residues processed: 49 average time/residue: 0.1954 time to fit residues: 13.4218 Evaluate side-chains 51 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 33 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 CYS 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 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 62 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 57 optimal weight: 0.0170 chunk 18 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 overall best weight: 1.0820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.079005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.060945 restraints weight = 20099.655| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.91 r_work: 0.2847 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1478 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= 0.188 Angle : 0.538 9.057 10343 Z= 0.284 Chirality : 0.035 0.147 1173 Planarity : 0.003 0.033 1048 Dihedral : 21.327 178.675 1859 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.26 % Allowed : 24.36 % 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 (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: 1.38 (0.33), residues: 658 helix: 2.65 (0.30), residues: 279 sheet: 0.15 (0.48), residues: 109 loop : -0.63 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 645 HIS 0.003 0.001 HIS A 609 PHE 0.013 0.001 PHE A 32 TYR 0.009 0.001 TYR A 22 ARG 0.005 0.000 ARG A 615 ********************** 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 53 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 34 time to evaluate : 0.691 Fit side-chains REVERT: A 202 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.7922 (t80) REVERT: A 481 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8750 (mt) REVERT: A 544 ARG cc_start: 0.8695 (ptp90) cc_final: 0.8484 (ptp90) REVERT: A 547 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.7989 (mttt) REVERT: A 798 TYR cc_start: 0.9145 (OUTLIER) cc_final: 0.7912 (m-80) REVERT: A 828 GLU cc_start: 0.5562 (OUTLIER) cc_final: 0.4015 (mm-30) outliers start: 19 outliers final: 13 residues processed: 48 average time/residue: 0.1905 time to fit residues: 12.9503 Evaluate side-chains 52 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 34 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 70 CYS 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 0.0470 chunk 7 optimal weight: 0.5980 chunk 70 optimal weight: 10.0000 chunk 32 optimal weight: 0.2980 chunk 60 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 635 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.081010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.062561 restraints weight = 19837.837| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.97 r_work: 0.2880 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7403 Z= 0.138 Angle : 0.514 8.724 10343 Z= 0.271 Chirality : 0.034 0.152 1173 Planarity : 0.003 0.032 1048 Dihedral : 21.255 177.882 1859 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.92 % Allowed : 24.70 % 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 (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: 1.37 (0.33), residues: 658 helix: 2.64 (0.30), residues: 281 sheet: 0.22 (0.48), residues: 109 loop : -0.70 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 640 HIS 0.001 0.000 HIS A 526 PHE 0.010 0.001 PHE A 32 TYR 0.010 0.001 TYR A 22 ARG 0.005 0.000 ARG A 615 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2909.21 seconds wall clock time: 54 minutes 38.21 seconds (3278.21 seconds total)