Starting phenix.real_space_refine on Thu Jul 2 07:12:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lcy_62996/07_2026/9lcy_62996_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lcy_62996/07_2026/9lcy_62996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lcy_62996/07_2026/9lcy_62996_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lcy_62996/07_2026/9lcy_62996_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lcy_62996/07_2026/9lcy_62996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lcy_62996/07_2026/9lcy_62996.map" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.151 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 56 5.49 5 S 21 5.16 5 C 4390 2.51 5 N 1323 2.21 5 O 1503 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7294 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 6145 Classifications: {'peptide': 835} Link IDs: {'PTRANS': 46, 'TRANS': 788} Chain: "B" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 570 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "C" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 578 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5828 SG CYS A 842 46.810 55.673 98.034 1.00 29.23 S ATOM 5850 SG CYS A 845 46.032 53.180 100.303 1.00 29.25 S Time building chain proxies: 1.45, per 1000 atoms: 0.20 Number of scatterers: 7294 At special positions: 0 Unit cell: (85.1067, 85.1067, 128.199, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 21 16.00 P 56 15.00 O 1503 8.00 N 1323 7.00 C 4390 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 374.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" ND1 HIS A 814 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 842 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 845 " 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1512 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 1 sheets defined 73.8% alpha, 3.4% beta 24 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 63 through 81 removed outlier: 6.900A pdb=" N GLN A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ASP A 76 " --> pdb=" O VAL A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 94 Processing helix chain 'A' and resid 97 through 113 removed outlier: 4.811A pdb=" N GLY A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N GLU A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 142 through 147 removed outlier: 3.715A pdb=" N THR A 147 " --> pdb=" O ARG A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 163 Processing helix chain 'A' and resid 166 through 184 removed outlier: 3.505A pdb=" N ALA A 170 " --> pdb=" O GLY A 166 " (cutoff:3.500A) Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 188 through 197 Processing helix chain 'A' and resid 200 through 217 Proline residue: A 213 - end of helix Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 234 through 252 Proline residue: A 247 - end of helix Processing helix chain 'A' and resid 256 through 265 Processing helix chain 'A' and resid 268 through 286 removed outlier: 3.682A pdb=" N ALA A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) Proline residue: A 281 - end of helix Processing helix chain 'A' and resid 290 through 299 Processing helix chain 'A' and resid 302 through 320 Proline residue: A 315 - end of helix Processing helix chain 'A' and resid 324 through 333 Processing helix chain 'A' and resid 336 through 354 Proline residue: A 349 - end of helix Processing helix chain 'A' and resid 358 through 367 Processing helix chain 'A' and resid 370 through 388 Proline residue: A 383 - end of helix removed outlier: 3.522A pdb=" N ALA A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 401 Processing helix chain 'A' and resid 404 through 422 Proline residue: A 417 - end of helix Processing helix chain 'A' and resid 426 through 435 Processing helix chain 'A' and resid 438 through 456 Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 460 through 469 Processing helix chain 'A' and resid 472 through 491 Proline residue: A 485 - end of helix Processing helix chain 'A' and resid 494 through 504 removed outlier: 4.408A pdb=" N HIS A 504 " --> pdb=" O ALA A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 522 Proline residue: A 519 - end of helix Processing helix chain 'A' and resid 528 through 537 Processing helix chain 'A' and resid 540 through 558 Proline residue: A 553 - end of helix Processing helix chain 'A' and resid 562 through 571 Processing helix chain 'A' and resid 574 through 592 Proline residue: A 587 - end of helix Processing helix chain 'A' and resid 596 through 605 Processing helix chain 'A' and resid 608 through 627 Proline residue: A 621 - end of helix Processing helix chain 'A' and resid 630 through 639 Processing helix chain 'A' and resid 642 through 660 Proline residue: A 655 - end of helix Processing helix chain 'A' and resid 664 through 673 Processing helix chain 'A' and resid 676 through 690 Processing helix chain 'A' and resid 692 through 702 Processing helix chain 'A' and resid 715 through 734 Processing helix chain 'A' and resid 737 through 752 removed outlier: 3.834A pdb=" N ASP A 741 " --> pdb=" O LEU A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 827 Processing helix chain 'A' and resid 842 through 853 removed outlier: 3.528A pdb=" N THR A 849 " --> pdb=" O CYS A 845 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ALA A 850 " --> pdb=" O ASN A 846 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N THR A 851 " --> pdb=" O THR A 847 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE A 852 " --> pdb=" O MET A 848 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 765 through 768 removed outlier: 4.434A pdb=" N ALA A 708 " --> pdb=" O GLY A 796 " (cutoff:3.500A) 406 hydrogen bonds defined for protein. 1209 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 57 hydrogen bonds 114 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 1.59 Time building geometry restraints manager: 0.77 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: 1777 1.33 - 1.45: 1503 1.45 - 1.57: 4112 1.57 - 1.69: 110 1.69 - 1.81: 25 Bond restraints: 7527 Sorted by residual: bond pdb=" C3' DG C 10 " pdb=" C2' DG C 10 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DA B -8 " pdb=" C2' DA B -8 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DC B 2 " pdb=" C2' DC B 2 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.60e+00 bond pdb=" C3' DT B -17 " pdb=" C2' DT B -17 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.60e+00 bond pdb=" C3' DT C 4 " pdb=" C2' DT C 4 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.45e+00 ... (remaining 7522 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 10146 1.45 - 2.91: 306 2.91 - 4.36: 25 4.36 - 5.81: 20 5.81 - 7.26: 1 Bond angle restraints: 10498 Sorted by residual: angle pdb=" N3 DT C -1 " pdb=" C4 DT C -1 " pdb=" O4 DT C -1 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.80e+01 angle pdb=" N3 DT C 18 " pdb=" C4 DT C 18 " pdb=" O4 DT C 18 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT B -7 " pdb=" C4 DT B -7 " pdb=" O4 DT B -7 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT B -17 " pdb=" C4 DT B -17 " pdb=" O4 DT B -17 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT B -11 " pdb=" C4 DT B -11 " pdb=" O4 DT B -11 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 ... (remaining 10493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 3635 16.75 - 33.51: 462 33.51 - 50.26: 204 50.26 - 67.01: 86 67.01 - 83.76: 9 Dihedral angle restraints: 4396 sinusoidal: 2040 harmonic: 2356 Sorted by residual: dihedral pdb=" CA LEU A 700 " pdb=" C LEU A 700 " pdb=" N MET A 701 " pdb=" CA MET A 701 " ideal model delta harmonic sigma weight residual 180.00 161.98 18.02 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA ARG A 550 " pdb=" C ARG A 550 " pdb=" N LEU A 551 " pdb=" CA LEU A 551 " ideal model delta harmonic sigma weight residual 180.00 -163.43 -16.57 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA ARG A 618 " pdb=" C ARG A 618 " pdb=" N LEU A 619 " pdb=" CA LEU A 619 " ideal model delta harmonic sigma weight residual -180.00 -164.25 -15.75 0 5.00e+00 4.00e-02 9.92e+00 ... (remaining 4393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 788 0.032 - 0.065: 300 0.065 - 0.097: 145 0.097 - 0.129: 31 0.129 - 0.161: 3 Chirality restraints: 1267 Sorted by residual: chirality pdb=" CA GLN A 718 " pdb=" N GLN A 718 " pdb=" C GLN A 718 " pdb=" CB GLN A 718 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" CA LEU A 663 " pdb=" N LEU A 663 " pdb=" C LEU A 663 " pdb=" CB LEU A 663 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CG LEU A 700 " pdb=" CB LEU A 700 " pdb=" CD1 LEU A 700 " pdb=" CD2 LEU A 700 " both_signs ideal model delta sigma weight residual False -2.59 -2.72 0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 1264 not shown) Planarity restraints: 1178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 717 " -0.009 2.00e-02 2.50e+03 1.98e-02 3.91e+00 pdb=" C LYS A 717 " 0.034 2.00e-02 2.50e+03 pdb=" O LYS A 717 " -0.013 2.00e-02 2.50e+03 pdb=" N GLN A 718 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 760 " 0.028 5.00e-02 4.00e+02 4.29e-02 2.95e+00 pdb=" N PRO A 761 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 761 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 761 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 562 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO A 563 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 563 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 563 " -0.023 5.00e-02 4.00e+02 ... (remaining 1175 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1043 2.76 - 3.29: 6733 3.29 - 3.83: 12432 3.83 - 4.36: 14915 4.36 - 4.90: 25040 Nonbonded interactions: 60163 Sorted by model distance: nonbonded pdb=" O CYS A 845 " pdb=" OG1 THR A 849 " model vdw 2.224 3.040 nonbonded pdb=" O VAL A 227 " pdb=" OG SER A 231 " model vdw 2.272 3.040 nonbonded pdb=" O VAL A 397 " pdb=" OG SER A 401 " model vdw 2.280 3.040 nonbonded pdb=" O VAL A 601 " pdb=" OG SER A 605 " model vdw 2.290 3.040 nonbonded pdb=" OH TYR A 809 " pdb=" OP1 DC B 2 " model vdw 2.325 3.040 ... (remaining 60158 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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.400 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 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 : 0.004 0.034 7530 Z= 0.325 Angle : 0.583 7.264 10498 Z= 0.420 Chirality : 0.043 0.161 1267 Planarity : 0.005 0.043 1178 Dihedral : 19.105 83.762 2884 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.29), residues: 833 helix: 1.05 (0.21), residues: 586 sheet: 0.13 (0.75), residues: 49 loop : -0.55 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 100 TYR 0.007 0.001 TYR A 834 PHE 0.002 0.000 PHE A 797 TRP 0.002 0.000 TRP A 96 HIS 0.003 0.001 HIS A 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.32 ( 7527) covalent geometry : angle 0.58331 / 0.42 (10498) hydrogen bonds : bond 0.14465 / 9.86 ( 463) hydrogen bonds : angle 6.10574 / 4.32 ( 1323) metal coordination : bond 0.00173 / 0.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.252 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.0851 time to fit residues: 8.7801 Evaluate side-chains 53 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.0270 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 GLN A 617 GLN A 661 HIS A 720 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.199643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.178963 restraints weight = 6290.205| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 0.66 r_work: 0.3539 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7530 Z= 0.141 Angle : 0.562 7.758 10498 Z= 0.314 Chirality : 0.041 0.121 1267 Planarity : 0.005 0.044 1178 Dihedral : 20.828 83.625 1476 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.61 % Allowed : 4.86 % Favored : 94.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.29), residues: 833 helix: 1.23 (0.21), residues: 595 sheet: 0.15 (0.76), residues: 49 loop : -0.37 (0.44), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 873 TYR 0.006 0.001 TYR A 834 PHE 0.003 0.001 PHE A 768 TRP 0.003 0.001 TRP A 142 HIS 0.003 0.001 HIS A 835 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 ( 7527) covalent geometry : angle 0.56198 / 0.31 (10498) hydrogen bonds : bond 0.03871 / 2.65 ( 463) hydrogen bonds : angle 4.44607 / 3.24 ( 1323) metal coordination : bond 0.00253 / 0.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.299 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 60 average time/residue: 0.0818 time to fit residues: 6.9015 Evaluate side-chains 47 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 GLN Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 745 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 80 optimal weight: 0.1980 chunk 82 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 53 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 chunk 81 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 661 HIS A 720 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.196390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.182544 restraints weight = 6375.916| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 0.69 r_work: 0.3589 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7530 Z= 0.130 Angle : 0.529 6.848 10498 Z= 0.292 Chirality : 0.040 0.121 1267 Planarity : 0.004 0.045 1178 Dihedral : 21.243 84.194 1476 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.61 % Allowed : 7.60 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.29), residues: 833 helix: 1.32 (0.21), residues: 594 sheet: 0.23 (0.77), residues: 49 loop : -0.47 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 810 TYR 0.006 0.001 TYR A 697 PHE 0.002 0.000 PHE A 797 TRP 0.002 0.001 TRP A 142 HIS 0.003 0.001 HIS A 835 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.13 ( 7527) covalent geometry : angle 0.52868 / 0.29 (10498) hydrogen bonds : bond 0.03215 / 2.23 ( 463) hydrogen bonds : angle 4.23280 / 3.09 ( 1323) metal coordination : bond 0.00174 / 0.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.231 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 51 average time/residue: 0.0917 time to fit residues: 6.4665 Evaluate side-chains 50 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 GLN Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 745 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 70 optimal weight: 0.0970 chunk 84 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 16 optimal weight: 0.0370 chunk 52 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 661 HIS A 720 ASN A 827 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.196690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.185455 restraints weight = 6435.911| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 0.54 r_work: 0.3641 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7530 Z= 0.123 Angle : 0.519 9.097 10498 Z= 0.285 Chirality : 0.039 0.115 1267 Planarity : 0.004 0.047 1178 Dihedral : 21.198 83.253 1476 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.76 % Allowed : 8.51 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.29), residues: 833 helix: 1.37 (0.21), residues: 594 sheet: 0.26 (0.77), residues: 49 loop : -0.48 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 702 TYR 0.006 0.001 TYR A 834 PHE 0.010 0.001 PHE A 852 TRP 0.002 0.001 TRP A 773 HIS 0.003 0.001 HIS A 835 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 ( 7527) covalent geometry : angle 0.51921 / 0.28 (10498) hydrogen bonds : bond 0.02975 / 2.05 ( 463) hydrogen bonds : angle 4.09601 / 2.99 ( 1323) metal coordination : bond 0.00171 / 0.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.162 Fit side-chains REVERT: A 806 TYR cc_start: 0.8574 (m-80) cc_final: 0.8245 (m-80) outliers start: 5 outliers final: 2 residues processed: 52 average time/residue: 0.0786 time to fit residues: 5.5799 Evaluate side-chains 44 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 833 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 53 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 720 ASN A 827 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.193166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.180784 restraints weight = 6384.255| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 0.61 r_work: 0.3579 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7530 Z= 0.187 Angle : 0.589 8.977 10498 Z= 0.317 Chirality : 0.042 0.155 1267 Planarity : 0.005 0.047 1178 Dihedral : 21.416 84.863 1476 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.06 % Allowed : 8.97 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.29), residues: 833 helix: 1.20 (0.21), residues: 593 sheet: -0.07 (0.71), residues: 52 loop : -0.66 (0.46), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.007 0.001 TYR A 697 PHE 0.006 0.001 PHE A 852 TRP 0.004 0.001 TRP A 773 HIS 0.004 0.001 HIS A 593 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 ( 7527) covalent geometry : angle 0.58895 / 0.32 (10498) hydrogen bonds : bond 0.03833 / 2.64 ( 463) hydrogen bonds : angle 4.26421 / 3.12 ( 1323) metal coordination : bond 0.00390 / 0.23 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.233 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 50 average time/residue: 0.0861 time to fit residues: 5.8601 Evaluate side-chains 48 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 858 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 35 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 3 optimal weight: 8.9990 chunk 51 optimal weight: 0.8980 chunk 30 optimal weight: 0.1980 chunk 82 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 720 ASN A 827 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.195243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.182432 restraints weight = 6402.674| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 0.61 r_work: 0.3606 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7530 Z= 0.133 Angle : 0.530 9.151 10498 Z= 0.289 Chirality : 0.040 0.117 1267 Planarity : 0.005 0.049 1178 Dihedral : 21.334 81.797 1476 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.76 % Allowed : 9.73 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.29), residues: 833 helix: 1.34 (0.22), residues: 592 sheet: -0.03 (0.75), residues: 50 loop : -0.48 (0.44), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 710 TYR 0.008 0.001 TYR A 697 PHE 0.006 0.001 PHE A 852 TRP 0.003 0.001 TRP A 773 HIS 0.003 0.001 HIS A 835 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 ( 7527) covalent geometry : angle 0.53010 / 0.29 (10498) hydrogen bonds : bond 0.03066 / 2.15 ( 463) hydrogen bonds : angle 4.12110 / 3.02 ( 1323) metal coordination : bond 0.00207 / 0.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.208 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 48 average time/residue: 0.0895 time to fit residues: 5.9465 Evaluate side-chains 48 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 858 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 70 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 0.0270 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 720 ASN A 827 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.195365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.182890 restraints weight = 6330.337| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 0.58 r_work: 0.3620 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7530 Z= 0.132 Angle : 0.526 9.379 10498 Z= 0.287 Chirality : 0.039 0.119 1267 Planarity : 0.005 0.048 1178 Dihedral : 21.290 80.630 1476 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.91 % Allowed : 10.03 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.29), residues: 833 helix: 1.37 (0.22), residues: 590 sheet: 0.01 (0.75), residues: 50 loop : -0.55 (0.44), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 710 TYR 0.009 0.001 TYR A 697 PHE 0.007 0.001 PHE A 852 TRP 0.003 0.001 TRP A 773 HIS 0.003 0.001 HIS A 835 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 ( 7527) covalent geometry : angle 0.52580 / 0.29 (10498) hydrogen bonds : bond 0.03075 / 2.14 ( 463) hydrogen bonds : angle 4.07731 / 2.99 ( 1323) metal coordination : bond 0.00205 / 0.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.167 Fit side-chains REVERT: A 806 TYR cc_start: 0.8548 (m-80) cc_final: 0.8147 (m-80) outliers start: 6 outliers final: 5 residues processed: 48 average time/residue: 0.0746 time to fit residues: 4.9947 Evaluate side-chains 47 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 827 ASN Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 858 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 70 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 72 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 54 optimal weight: 0.2980 chunk 8 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 720 ASN A 827 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.195601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.183145 restraints weight = 6385.592| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 0.57 r_work: 0.3621 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7530 Z= 0.129 Angle : 0.522 9.500 10498 Z= 0.285 Chirality : 0.039 0.118 1267 Planarity : 0.005 0.048 1178 Dihedral : 21.279 80.683 1476 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.06 % Allowed : 10.18 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.29), residues: 833 helix: 1.40 (0.22), residues: 590 sheet: 0.05 (0.76), residues: 50 loop : -0.51 (0.44), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 810 TYR 0.009 0.001 TYR A 697 PHE 0.006 0.001 PHE A 852 TRP 0.002 0.001 TRP A 142 HIS 0.003 0.001 HIS A 835 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 ( 7527) covalent geometry : angle 0.52212 / 0.28 (10498) hydrogen bonds : bond 0.02999 / 2.09 ( 463) hydrogen bonds : angle 4.05325 / 2.97 ( 1323) metal coordination : bond 0.00204 / 0.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.240 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 47 average time/residue: 0.0712 time to fit residues: 4.7573 Evaluate side-chains 46 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 858 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 14 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 720 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.195060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.183084 restraints weight = 6316.793| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 0.56 r_work: 0.3625 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7530 Z= 0.138 Angle : 0.532 9.857 10498 Z= 0.289 Chirality : 0.039 0.124 1267 Planarity : 0.005 0.048 1178 Dihedral : 21.285 81.109 1476 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.91 % Allowed : 10.33 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.29), residues: 833 helix: 1.38 (0.22), residues: 590 sheet: 0.08 (0.76), residues: 50 loop : -0.52 (0.45), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 346 TYR 0.009 0.001 TYR A 697 PHE 0.006 0.001 PHE A 852 TRP 0.003 0.001 TRP A 773 HIS 0.003 0.001 HIS A 835 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 ( 7527) covalent geometry : angle 0.53190 / 0.29 (10498) hydrogen bonds : bond 0.03104 / 2.16 ( 463) hydrogen bonds : angle 4.06255 / 2.98 ( 1323) metal coordination : bond 0.00251 / 0.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.139 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 49 average time/residue: 0.0714 time to fit residues: 4.9264 Evaluate side-chains 47 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 858 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 79 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 0.0170 chunk 40 optimal weight: 0.1980 chunk 23 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 53 optimal weight: 0.6980 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 720 ASN A 827 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.197089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.186676 restraints weight = 6290.076| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 0.75 r_work: 0.3590 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7530 Z= 0.113 Angle : 0.507 9.952 10498 Z= 0.277 Chirality : 0.038 0.118 1267 Planarity : 0.005 0.048 1178 Dihedral : 21.184 80.650 1476 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.91 % Allowed : 10.79 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.30), residues: 833 helix: 1.45 (0.22), residues: 591 sheet: 0.24 (0.78), residues: 50 loop : -0.46 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 678 TYR 0.009 0.001 TYR A 697 PHE 0.005 0.000 PHE A 852 TRP 0.003 0.001 TRP A 96 HIS 0.002 0.000 HIS A 835 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.11 ( 7527) covalent geometry : angle 0.50695 / 0.28 (10498) hydrogen bonds : bond 0.02666 / 1.87 ( 463) hydrogen bonds : angle 3.96167 / 2.90 ( 1323) metal coordination : bond 0.00092 / 0.06 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.178 Fit side-chains REVERT: A 806 TYR cc_start: 0.8547 (m-80) cc_final: 0.8150 (m-80) REVERT: A 810 ARG cc_start: 0.8384 (mtt180) cc_final: 0.8160 (mtt180) outliers start: 6 outliers final: 6 residues processed: 50 average time/residue: 0.0753 time to fit residues: 5.2786 Evaluate side-chains 51 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 827 ASN Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 858 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 720 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.197067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.172770 restraints weight = 6316.676| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 1.15 r_work: 0.3460 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.140 7530 Z= 0.204 Angle : 0.952 59.194 10498 Z= 0.572 Chirality : 0.039 0.239 1267 Planarity : 0.005 0.048 1178 Dihedral : 21.191 80.697 1476 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.04 % Favored : 97.84 % Rotamer: Outliers : 0.76 % Allowed : 11.09 % Favored : 88.15 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.30), residues: 833 helix: 1.44 (0.22), residues: 591 sheet: 0.25 (0.78), residues: 50 loop : -0.47 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 810 TYR 0.009 0.001 TYR A 697 PHE 0.005 0.001 PHE A 852 TRP 0.003 0.001 TRP A 96 HIS 0.003 0.000 HIS A 835 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.20 ( 7527) covalent geometry : angle 0.95219 / 0.57 (10498) hydrogen bonds : bond 0.02714 / 1.91 ( 463) hydrogen bonds : angle 3.94804 / 2.90 ( 1323) metal coordination : bond 0.00171 / 0.10 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1726.90 seconds wall clock time: 30 minutes 12.11 seconds (1812.11 seconds total)