Starting phenix.real_space_refine on Tue Aug 4 23:29:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lcy_62996/08_2026/9lcy_62996_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lcy_62996/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9lcy_62996/08_2026/9lcy_62996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lcy_62996/08_2026/9lcy_62996.map" model { file = "/net/cci-nas-00/data/ceres_data/9lcy_62996/08_2026/9lcy_62996_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lcy_62996/08_2026/9lcy_62996_neut.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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: 1.86, per 1000 atoms: 0.26 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: 0.44 Conformation dependent library (CDL) restraints added in 340.8 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: 0.92 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: 1.58 Time building geometry restraints manager: 0.58 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: 1.400 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.510 Find NCS groups from input model: 0.020 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.180 ------------------------------------------------------------------------------- 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 : 0.585 7.264 10498 Z= 0.422 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 / 0.33 ( 7527) covalent geometry : angle 0.58540 / 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 : 0.238 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.0845 time to fit residues: 8.7872 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 : 0.205 ------------------------------------------------------------------------------- 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: 1.9990 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 = 0.4121 r_free = 0.4121 target = 0.199817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 142)---------------| | r_work = 0.3727 r_free = 0.3727 target = 0.158269 restraints weight = 6294.120| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 1.14 r_work: 0.3446 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7530 Z= 0.143 Angle : 0.575 8.092 10498 Z= 0.318 Chirality : 0.042 0.129 1267 Planarity : 0.005 0.044 1178 Dihedral : 20.900 83.549 1476 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.46 % Allowed : 5.02 % 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: 1.07 (0.29), residues: 833 helix: 1.19 (0.21), residues: 596 sheet: 0.15 (0.76), residues: 49 loop : -0.47 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 873 TYR 0.006 0.001 TYR A 697 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 0.00283 / 0.14 ( 7527) covalent geometry : angle 0.57451 / 0.32 (10498) hydrogen bonds : bond 0.03698 / 2.53 ( 463) hydrogen bonds : angle 4.41850 / 3.22 ( 1323) metal coordination : bond 0.00254 / 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 60 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.143 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 58 average time/residue: 0.0841 time to fit residues: 6.8802 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 : 0.151 ------------------------------------------------------------------------------- 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: 3.9990 chunk 83 optimal weight: 7.9990 chunk 80 optimal weight: 0.4980 chunk 82 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 chunk 53 optimal weight: 0.0980 chunk 40 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.4087 r_free = 0.4087 target = 0.195700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.181107 restraints weight = 6368.056| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 0.74 r_work: 0.3555 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1152 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= 0.135 Angle : 0.535 6.758 10498 Z= 0.295 Chirality : 0.040 0.129 1267 Planarity : 0.004 0.045 1178 Dihedral : 21.173 84.068 1476 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.91 % Allowed : 7.29 % 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: 1.24 (0.29), residues: 833 helix: 1.33 (0.21), residues: 595 sheet: 0.18 (0.77), residues: 49 loop : -0.45 (0.44), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 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 773 HIS 0.003 0.001 HIS A 835 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 ( 7527) covalent geometry : angle 0.53477 / 0.29 (10498) hydrogen bonds : bond 0.03390 / 2.34 ( 463) hydrogen bonds : angle 4.25805 / 3.11 ( 1323) metal coordination : bond 0.00204 / 0.12 ( 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 56 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.221 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 52 average time/residue: 0.0727 time to fit residues: 5.2203 Evaluate side-chains 46 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 827 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 70 optimal weight: 0.4980 chunk 84 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 85 optimal weight: 9.9990 chunk 16 optimal weight: 0.0980 chunk 52 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 86 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 17 optimal weight: 0.0980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.4100 r_free = 0.4100 target = 0.196886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 104)---------------| | r_work = 0.3835 r_free = 0.3835 target = 0.170698 restraints weight = 6435.893| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 1.25 r_work: 0.3452 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1253 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= 0.118 Angle : 0.518 8.489 10498 Z= 0.285 Chirality : 0.039 0.117 1267 Planarity : 0.004 0.046 1178 Dihedral : 21.160 83.587 1476 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.61 % Allowed : 8.51 % Favored : 90.88 % 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: 1.34 (0.29), residues: 833 helix: 1.41 (0.22), residues: 594 sheet: 0.24 (0.77), residues: 49 loop : -0.44 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 702 TYR 0.007 0.001 TYR A 697 PHE 0.010 0.001 PHE A 852 TRP 0.002 0.001 TRP A 96 HIS 0.003 0.000 HIS A 835 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.12 ( 7527) covalent geometry : angle 0.51790 / 0.28 (10498) hydrogen bonds : bond 0.02962 / 2.05 ( 463) hydrogen bonds : angle 4.13629 / 3.02 ( 1323) metal coordination : bond 0.00128 / 0.07 ( 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 49 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.239 Fit side-chains REVERT: A 701 MET cc_start: 0.8888 (mmm) cc_final: 0.8548 (mmm) outliers start: 4 outliers final: 2 residues processed: 46 average time/residue: 0.0982 time to fit residues: 6.1073 Evaluate side-chains 43 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 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: 0.3980 chunk 4 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 5 optimal weight: 0.0020 overall best weight: 0.5588 ------------------------------------------------------------------------------- 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 = 0.4097 r_free = 0.4097 target = 0.196851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.185624 restraints weight = 6384.692| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 0.55 r_work: 0.3638 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1380 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 : 0.515 7.481 10498 Z= 0.283 Chirality : 0.039 0.117 1267 Planarity : 0.004 0.046 1178 Dihedral : 21.175 83.245 1476 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.76 % Allowed : 8.97 % Favored : 90.27 % 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: 1.37 (0.29), residues: 833 helix: 1.47 (0.22), residues: 590 sheet: 0.02 (0.73), residues: 53 loop : -0.45 (0.45), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 346 TYR 0.007 0.001 TYR A 697 PHE 0.008 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 0.00238 / 0.12 ( 7527) covalent geometry : angle 0.51524 / 0.28 (10498) hydrogen bonds : bond 0.02947 / 2.04 ( 463) hydrogen bonds : angle 4.06161 / 2.97 ( 1323) metal coordination : bond 0.00155 / 0.09 ( 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 52 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.192 Fit side-chains REVERT: A 702 ARG cc_start: 0.7876 (mtt180) cc_final: 0.7640 (mmm160) REVERT: A 806 TYR cc_start: 0.8571 (m-80) cc_final: 0.8251 (m-80) outliers start: 5 outliers final: 4 residues processed: 51 average time/residue: 0.0732 time to fit residues: 5.1252 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 : 0.158 ------------------------------------------------------------------------------- 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: 0.7980 chunk 63 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 3 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 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 = 0.4087 r_free = 0.4087 target = 0.195939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.183601 restraints weight = 6408.766| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 0.59 r_work: 0.3614 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1445 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= 0.132 Angle : 0.528 9.437 10498 Z= 0.287 Chirality : 0.039 0.124 1267 Planarity : 0.004 0.047 1178 Dihedral : 21.193 80.510 1476 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.91 % Allowed : 8.97 % Favored : 90.12 % 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: 1.32 (0.29), residues: 833 helix: 1.45 (0.22), residues: 590 sheet: 0.10 (0.72), residues: 52 loop : -0.57 (0.44), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 346 TYR 0.007 0.001 TYR A 697 PHE 0.007 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 0.00271 / 0.13 ( 7527) covalent geometry : angle 0.52784 / 0.29 (10498) hydrogen bonds : bond 0.03026 / 2.10 ( 463) hydrogen bonds : angle 4.05764 / 2.97 ( 1323) metal coordination : bond 0.00210 / 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 55 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.191 Fit side-chains REVERT: A 702 ARG cc_start: 0.7888 (mtt180) cc_final: 0.7628 (mmm160) REVERT: A 806 TYR cc_start: 0.8578 (m-80) cc_final: 0.8184 (m-80) outliers start: 6 outliers final: 5 residues processed: 53 average time/residue: 0.0821 time to fit residues: 6.1074 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 : 0.195 ------------------------------------------------------------------------------- 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 827 ASN 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: 3.9990 chunk 48 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 0.1980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4084 r_free = 0.4084 target = 0.195592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.182965 restraints weight = 6364.565| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 0.58 r_work: 0.3633 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1496 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= 0.136 Angle : 0.531 9.269 10498 Z= 0.289 Chirality : 0.039 0.124 1267 Planarity : 0.005 0.048 1178 Dihedral : 21.202 80.299 1476 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.91 % Allowed : 9.57 % 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: 1.33 (0.29), residues: 833 helix: 1.46 (0.22), residues: 590 sheet: 0.12 (0.73), residues: 52 loop : -0.56 (0.44), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 346 TYR 0.012 0.001 TYR A 877 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 0.00283 / 0.14 ( 7527) covalent geometry : angle 0.53124 / 0.29 (10498) hydrogen bonds : bond 0.03055 / 2.12 ( 463) hydrogen bonds : angle 4.05314 / 2.97 ( 1323) metal coordination : bond 0.00234 / 0.13 ( 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 : 0.203 Fit side-chains REVERT: A 702 ARG cc_start: 0.7865 (mtt180) cc_final: 0.7595 (mmm160) outliers start: 6 outliers final: 4 residues processed: 48 average time/residue: 0.0805 time to fit residues: 5.4526 Evaluate side-chains 46 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 70 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 26 optimal weight: 0.0870 chunk 72 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.4091 r_free = 0.4091 target = 0.196285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.182010 restraints weight = 6398.391| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 0.67 r_work: 0.3583 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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 : 0.003 0.029 7530 Z= 0.125 Angle : 0.521 9.621 10498 Z= 0.283 Chirality : 0.039 0.117 1267 Planarity : 0.004 0.048 1178 Dihedral : 21.181 79.977 1476 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.61 % Allowed : 9.88 % 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: 1.36 (0.29), residues: 833 helix: 1.47 (0.22), residues: 590 sheet: 0.08 (0.73), residues: 53 loop : -0.50 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 516 TYR 0.013 0.001 TYR A 877 PHE 0.006 0.001 PHE A 852 TRP 0.004 0.001 TRP A 773 HIS 0.003 0.001 HIS A 835 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 ( 7527) covalent geometry : angle 0.52096 / 0.28 (10498) hydrogen bonds : bond 0.02874 / 2.01 ( 463) hydrogen bonds : angle 3.99384 / 2.93 ( 1323) metal coordination : bond 0.00177 / 0.10 ( 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 48 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.184 Fit side-chains REVERT: A 806 TYR cc_start: 0.8555 (m-80) cc_final: 0.8201 (m-80) outliers start: 4 outliers final: 3 residues processed: 47 average time/residue: 0.0907 time to fit residues: 5.8784 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 : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 711 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: 0.5980 chunk 1 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 50 optimal weight: 0.3980 chunk 71 optimal weight: 0.0010 chunk 64 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 78 optimal weight: 0.8980 overall best weight: 0.5586 ------------------------------------------------------------------------------- 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 = 0.4092 r_free = 0.4092 target = 0.196445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.183326 restraints weight = 6338.813| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 0.60 r_work: 0.3635 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1632 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= 0.122 Angle : 0.517 9.685 10498 Z= 0.281 Chirality : 0.039 0.118 1267 Planarity : 0.004 0.048 1178 Dihedral : 21.154 79.026 1476 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.76 % Allowed : 9.88 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.30), residues: 833 helix: 1.49 (0.22), residues: 591 sheet: 0.12 (0.73), residues: 53 loop : -0.47 (0.45), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 346 TYR 0.011 0.001 TYR A 877 PHE 0.005 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 0.00240 / 0.12 ( 7527) covalent geometry : angle 0.51679 / 0.28 (10498) hydrogen bonds : bond 0.02841 / 1.98 ( 463) hydrogen bonds : angle 3.97046 / 2.91 ( 1323) metal coordination : bond 0.00194 / 0.12 ( 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: 5 poor density : 45 time to evaluate : 0.290 Fit side-chains REVERT: A 806 TYR cc_start: 0.8546 (m-80) cc_final: 0.8178 (m-80) outliers start: 5 outliers final: 4 residues processed: 48 average time/residue: 0.0782 time to fit residues: 5.3585 Evaluate side-chains 45 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 1.9990 chunk 71 optimal weight: 0.0570 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 0.0980 chunk 40 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 = 0.4094 r_free = 0.4094 target = 0.196670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.171603 restraints weight = 6315.881| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 1.09 r_work: 0.3465 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1678 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= 0.122 Angle : 0.519 10.888 10498 Z= 0.281 Chirality : 0.039 0.118 1267 Planarity : 0.004 0.048 1178 Dihedral : 21.147 79.904 1476 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.76 % Allowed : 10.49 % 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: 1.42 (0.30), residues: 833 helix: 1.49 (0.22), residues: 591 sheet: 0.20 (0.74), residues: 53 loop : -0.43 (0.45), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 810 TYR 0.011 0.001 TYR A 877 PHE 0.005 0.001 PHE A 852 TRP 0.004 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 0.51932 / 0.28 (10498) hydrogen bonds : bond 0.02814 / 1.96 ( 463) hydrogen bonds : angle 3.95691 / 2.89 ( 1323) metal coordination : bond 0.00185 / 0.11 ( 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 47 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.238 Fit side-chains REVERT: A 806 TYR cc_start: 0.8563 (m-80) cc_final: 0.8189 (m-80) outliers start: 5 outliers final: 5 residues processed: 44 average time/residue: 0.0906 time to fit residues: 5.6283 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 : 0.249 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 chunk 33 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4091 r_free = 0.4091 target = 0.196826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.183496 restraints weight = 6343.064| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 0.61 r_work: 0.3611 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.144 7530 Z= 0.200 Angle : 0.962 59.162 10498 Z= 0.575 Chirality : 0.039 0.250 1267 Planarity : 0.005 0.048 1178 Dihedral : 21.156 79.930 1476 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.92 % Favored : 97.96 % Rotamer: Outliers : 0.76 % Allowed : 10.64 % Favored : 88.60 % 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: 1.41 (0.30), residues: 833 helix: 1.48 (0.22), residues: 591 sheet: 0.20 (0.74), residues: 53 loop : -0.44 (0.45), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 810 TYR 0.010 0.001 TYR A 877 PHE 0.005 0.001 PHE A 852 TRP 0.004 0.001 TRP A 773 HIS 0.003 0.001 HIS A 835 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.20 ( 7527) covalent geometry : angle 0.96235 / 0.57 (10498) hydrogen bonds : bond 0.02832 / 1.97 ( 463) hydrogen bonds : angle 3.94167 / 2.89 ( 1323) metal coordination : bond 0.00205 / 0.12 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1819.43 seconds wall clock time: 31 minutes 43.83 seconds (1903.83 seconds total)