Starting phenix.real_space_refine on Sat Dec 28 00:16:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xca_38238/12_2024/8xca_38238_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xca_38238/12_2024/8xca_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_38238/12_2024/8xca_38238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xca_38238/12_2024/8xca_38238.map" model { file = "/net/cci-nas-00/data/ceres_data/8xca_38238/12_2024/8xca_38238_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xca_38238/12_2024/8xca_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-5532/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: 6.74, per 1000 atoms: 0.95 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: 2.12 Conformation dependent library (CDL) restraints added in 640.9 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: 2.86 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: 3.03 Time building geometry restraints manager: 2.41 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: 3.730 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.100 Find NCS groups from input model: 0.060 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.290 ------------------------------------------------------------------------------- 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 : 0.728 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 36 average time/residue: 0.2222 time to fit residues: 11.3370 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 : 0.823 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 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 : 0.718 Fit side-chains REVERT: A 202 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.7872 (t80) REVERT: A 219 MET cc_start: 0.9097 (tpp) cc_final: 0.8821 (tpp) REVERT: A 481 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8719 (mt) outliers start: 15 outliers final: 9 residues processed: 47 average time/residue: 0.2056 time to fit residues: 13.4872 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 : 0.656 ------------------------------------------------------------------------------- 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 36 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 59 optimal weight: 0.3980 chunk 65 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.0962 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= 0.246 Angle : 0.520 6.462 10343 Z= 0.279 Chirality : 0.036 0.151 1173 Planarity : 0.004 0.032 1048 Dihedral : 21.254 178.540 1859 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.95 % Allowed : 22.98 % 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: 1.32 (0.33), residues: 658 helix: 2.62 (0.29), residues: 279 sheet: 0.08 (0.48), residues: 109 loop : -0.67 (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 0.008 0.001 PHE A 537 TYR 0.011 0.001 TYR A 538 ARG 0.002 0.000 ARG A 527 *********************** 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 58 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 35 time to evaluate : 0.652 Fit side-chains REVERT: A 202 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.7995 (t80) REVERT: A 547 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8103 (mttt) REVERT: A 635 ASN cc_start: 0.9102 (m-40) cc_final: 0.8887 (m-40) outliers start: 23 outliers final: 10 residues processed: 53 average time/residue: 0.2130 time to fit residues: 15.1478 Evaluate side-chains 44 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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 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 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 65 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 63 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 58 optimal weight: 0.7980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7403 Z= 0.332 Angle : 0.560 6.023 10343 Z= 0.299 Chirality : 0.037 0.164 1173 Planarity : 0.004 0.034 1048 Dihedral : 21.320 179.018 1859 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.29 % Allowed : 23.33 % 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: 1.26 (0.33), residues: 658 helix: 2.58 (0.30), residues: 279 sheet: 0.03 (0.47), residues: 109 loop : -0.71 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 720 HIS 0.004 0.001 HIS A 609 PHE 0.009 0.001 PHE A 32 TYR 0.012 0.001 TYR A 538 ARG 0.004 0.000 ARG A 544 *********************** 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 59 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 34 time to evaluate : 0.733 Fit side-chains REVERT: A 202 PHE cc_start: 0.8701 (OUTLIER) cc_final: 0.8094 (t80) REVERT: A 626 MET cc_start: 0.9240 (tpt) cc_final: 0.8851 (tpt) REVERT: A 635 ASN cc_start: 0.9140 (m-40) cc_final: 0.8834 (m-40) outliers start: 25 outliers final: 18 residues processed: 54 average time/residue: 0.2080 time to fit residues: 15.4962 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 : 0.752 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 40 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 23 optimal weight: 0.2980 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7403 Z= 0.227 Angle : 0.521 5.958 10343 Z= 0.280 Chirality : 0.036 0.153 1173 Planarity : 0.003 0.033 1048 Dihedral : 21.321 178.462 1859 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.29 % Allowed : 23.33 % 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: 1.31 (0.33), residues: 658 helix: 2.66 (0.30), residues: 279 sheet: 0.04 (0.48), residues: 109 loop : -0.71 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 640 HIS 0.003 0.001 HIS A 609 PHE 0.010 0.001 PHE A 202 TYR 0.010 0.001 TYR A 605 ARG 0.006 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 58 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 33 time to evaluate : 0.742 Fit side-chains REVERT: A 202 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.8026 (t80) REVERT: A 547 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8117 (mttt) REVERT: A 635 ASN cc_start: 0.9141 (m-40) cc_final: 0.8802 (m-40) outliers start: 25 outliers final: 17 residues processed: 53 average time/residue: 0.2213 time to fit residues: 16.1255 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 : 0.728 ------------------------------------------------------------------------------- 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 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 501 SER 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 798 TYR 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 63 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 58 optimal weight: 0.9980 chunk 32 optimal weight: 0.3980 chunk 5 optimal weight: 7.9990 chunk 23 optimal weight: 0.0470 chunk 37 optimal weight: 0.0770 chunk 68 optimal weight: 6.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7403 Z= 0.134 Angle : 0.491 5.786 10343 Z= 0.264 Chirality : 0.034 0.152 1173 Planarity : 0.003 0.032 1048 Dihedral : 21.251 178.107 1859 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.09 % Allowed : 24.70 % 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: 1.38 (0.33), residues: 658 helix: 2.71 (0.30), residues: 281 sheet: 0.16 (0.48), residues: 109 loop : -0.75 (0.37), 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 609 PHE 0.012 0.001 PHE A 202 TYR 0.009 0.001 TYR A 605 ARG 0.004 0.000 ARG A 615 *********************** 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 57 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 39 time to evaluate : 0.838 Fit side-chains revert: symmetry clash REVERT: A 202 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.7822 (t80) REVERT: A 544 ARG cc_start: 0.8479 (mtm-85) cc_final: 0.8251 (mtm180) REVERT: A 798 TYR cc_start: 0.9126 (OUTLIER) cc_final: 0.7758 (m-80) outliers start: 18 outliers final: 12 residues processed: 52 average time/residue: 0.2446 time to fit residues: 17.3053 Evaluate side-chains 48 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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 547 LYS 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 7 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 32 optimal weight: 0.0970 chunk 43 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 1.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 7403 Z= 0.277 Angle : 0.523 5.644 10343 Z= 0.281 Chirality : 0.036 0.160 1173 Planarity : 0.003 0.032 1048 Dihedral : 21.266 178.991 1859 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % 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: 1.44 (0.33), residues: 658 helix: 2.75 (0.30), residues: 279 sheet: 0.15 (0.48), residues: 109 loop : -0.65 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 229 HIS 0.003 0.001 HIS A 609 PHE 0.010 0.001 PHE A 202 TYR 0.011 0.001 TYR A 538 ARG 0.003 0.000 ARG A 615 *********************** 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 50 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 32 time to evaluate : 0.717 Fit side-chains revert: symmetry clash REVERT: A 202 PHE cc_start: 0.8607 (OUTLIER) cc_final: 0.8028 (t80) REVERT: A 828 GLU cc_start: 0.5543 (OUTLIER) cc_final: 0.4133 (mm-30) outliers start: 18 outliers final: 12 residues processed: 46 average time/residue: 0.2025 time to fit residues: 13.0977 Evaluate side-chains 45 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 31 time to evaluate : 0.708 ------------------------------------------------------------------------------- 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 501 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 42 optimal weight: 0.0870 chunk 21 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7403 Z= 0.286 Angle : 0.540 8.200 10343 Z= 0.289 Chirality : 0.036 0.166 1173 Planarity : 0.004 0.032 1048 Dihedral : 21.339 178.754 1859 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.77 % Allowed : 23.84 % 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: 1.40 (0.33), residues: 658 helix: 2.70 (0.30), residues: 279 sheet: 0.09 (0.48), residues: 109 loop : -0.63 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 720 HIS 0.004 0.001 HIS A 609 PHE 0.009 0.001 PHE A 202 TYR 0.011 0.001 TYR A 538 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 55 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 33 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: A 202 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.8084 (t80) REVERT: A 805 TRP cc_start: 0.6614 (OUTLIER) cc_final: 0.5983 (m-10) REVERT: A 828 GLU cc_start: 0.5611 (OUTLIER) cc_final: 0.4279 (mm-30) outliers start: 22 outliers final: 16 residues processed: 50 average time/residue: 0.1879 time to fit residues: 13.3657 Evaluate side-chains 50 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 31 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 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 446 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 42 optimal weight: 0.0070 overall best weight: 0.9604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7403 Z= 0.179 Angle : 0.522 8.349 10343 Z= 0.278 Chirality : 0.035 0.164 1173 Planarity : 0.003 0.032 1048 Dihedral : 21.334 178.411 1859 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.77 % Allowed : 24.01 % 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: 1.40 (0.33), residues: 658 helix: 2.65 (0.30), residues: 279 sheet: 0.19 (0.48), residues: 109 loop : -0.61 (0.37), residues: 270 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 0.011 0.001 PHE A 202 TYR 0.009 0.001 TYR A 605 ARG 0.014 0.000 ARG A 544 *********************** 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 55 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 33 time to evaluate : 0.718 Fit side-chains revert: symmetry clash REVERT: A 202 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.8000 (t80) REVERT: A 547 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8033 (mttt) REVERT: A 828 GLU cc_start: 0.5479 (OUTLIER) cc_final: 0.4079 (mm-30) outliers start: 22 outliers final: 17 residues processed: 51 average time/residue: 0.1924 time to fit residues: 13.9013 Evaluate side-chains 50 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 30 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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 209 HIS Chi-restraints excluded: chain A residue 235 ARG 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 446 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 32 optimal weight: 0.0980 chunk 48 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 35 optimal weight: 0.2980 chunk 46 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7403 Z= 0.279 Angle : 0.553 8.808 10343 Z= 0.294 Chirality : 0.037 0.176 1173 Planarity : 0.004 0.032 1048 Dihedral : 21.348 179.015 1859 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.60 % Allowed : 24.01 % 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: 1.43 (0.33), residues: 658 helix: 2.68 (0.30), residues: 279 sheet: 0.20 (0.49), residues: 109 loop : -0.60 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 741 HIS 0.003 0.001 HIS A 609 PHE 0.010 0.001 PHE A 202 TYR 0.012 0.001 TYR A 538 ARG 0.006 0.000 ARG A 544 ********************** 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 51 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 30 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: A 202 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.8079 (t80) REVERT: A 805 TRP cc_start: 0.6621 (OUTLIER) cc_final: 0.5989 (m-10) REVERT: A 828 GLU cc_start: 0.5621 (OUTLIER) cc_final: 0.4262 (mm-30) outliers start: 21 outliers final: 18 residues processed: 47 average time/residue: 0.2244 time to fit residues: 14.3956 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 : 0.679 ------------------------------------------------------------------------------- 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 209 HIS Chi-restraints excluded: chain A residue 235 ARG 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 446 VAL 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 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 53 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 24 optimal weight: 0.0470 chunk 59 optimal weight: 1.9990 chunk 7 optimal weight: 0.0470 chunk 10 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 3 optimal weight: 0.0270 chunk 41 optimal weight: 3.9990 overall best weight: 0.4034 ------------------------------------------------------------------------------- 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 = 0.3425 r_free = 0.3425 target = 0.080581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.062607 restraints weight = 19510.711| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.89 r_work: 0.2876 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7403 Z= 0.139 Angle : 0.514 7.118 10343 Z= 0.274 Chirality : 0.035 0.165 1173 Planarity : 0.003 0.032 1048 Dihedral : 21.327 177.936 1859 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.09 % Allowed : 24.53 % 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: 1.46 (0.33), residues: 658 helix: 2.66 (0.30), residues: 279 sheet: 0.32 (0.49), residues: 109 loop : -0.59 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 640 HIS 0.002 0.000 HIS A 526 PHE 0.017 0.001 PHE A 32 TYR 0.009 0.001 TYR A 605 ARG 0.013 0.000 ARG A 544 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1600.80 seconds wall clock time: 30 minutes 30.72 seconds (1830.72 seconds total)