Starting phenix.real_space_refine on Tue Aug 4 21:12:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q3f_72192/08_2026/9q3f_72192.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q3f_72192/08_2026/9q3f_72192.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9q3f_72192/08_2026/9q3f_72192.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q3f_72192/08_2026/9q3f_72192.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q3f_72192/08_2026/9q3f_72192.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q3f_72192/08_2026/9q3f_72192.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 39 5.16 5 C 4195 2.51 5 N 1186 2.21 5 O 1187 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: 6615 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 801, 6438 Classifications: {'peptide': 801} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 747} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 177 Classifications: {'RNA': 8} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 7} Link IDs: {'rna2p': 1, 'rna3p': 6} Time building chain proxies: 1.59, per 1000 atoms: 0.24 Number of scatterers: 6615 At special positions: 0 Unit cell: (75.264, 93.184, 107.968, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 39 16.00 P 8 15.00 O 1187 8.00 N 1186 7.00 C 4195 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: 0.55 Conformation dependent library (CDL) restraints added in 342.8 milliseconds 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 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: 24 helices and 10 sheets defined 35.1% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 65 through 80 Processing helix chain 'A' and resid 80 through 85 removed outlier: 3.896A pdb=" N ILE A 84 " --> pdb=" O PHE A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 147 Processing helix chain 'A' and resid 153 through 164 Processing helix chain 'A' and resid 165 through 172 Processing helix chain 'A' and resid 226 through 236 Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 304 through 314 Processing helix chain 'A' and resid 354 through 366 Processing helix chain 'A' and resid 368 through 384 removed outlier: 4.059A pdb=" N SER A 384 " --> pdb=" O MET A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 388 through 395 Processing helix chain 'A' and resid 461 through 478 removed outlier: 3.875A pdb=" N LYS A 465 " --> pdb=" O GLU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 509 Processing helix chain 'A' and resid 524 through 535 Processing helix chain 'A' and resid 546 through 551 Processing helix chain 'A' and resid 553 through 569 removed outlier: 3.855A pdb=" N VAL A 566 " --> pdb=" O LEU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 586 removed outlier: 3.928A pdb=" N PHE A 584 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN A 585 " --> pdb=" O ALA A 582 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN A 586 " --> pdb=" O VAL A 583 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 581 through 586' Processing helix chain 'A' and resid 638 through 655 Processing helix chain 'A' and resid 672 through 692 removed outlier: 3.887A pdb=" N ILE A 676 " --> pdb=" O GLN A 672 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 691 " --> pdb=" O ALA A 687 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU A 692 " --> pdb=" O CYS A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 784 Processing helix chain 'A' and resid 797 through 815 removed outlier: 3.570A pdb=" N VAL A 815 " --> pdb=" O ARG A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 844 removed outlier: 4.387A pdb=" N ALA A 840 " --> pdb=" O PRO A 836 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LYS A 841 " --> pdb=" O GLN A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 850 Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 35 Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 405 removed outlier: 3.728A pdb=" N VAL A 405 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 194 through 202 removed outlier: 3.715A pdb=" N SER A 217 " --> pdb=" O GLY A 198 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N MET A 210 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS A 397 " --> pdb=" O ASP A 46 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AA5, first strand: chain 'A' and resid 112 through 113 Processing sheet with id=AA6, first strand: chain 'A' and resid 280 through 281 removed outlier: 4.402A pdb=" N ASN A 280 " --> pdb=" O GLN A 326 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN A 326 " --> pdb=" O ASN A 280 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 415 through 416 Processing sheet with id=AA8, first strand: chain 'A' and resid 489 through 490 removed outlier: 7.297A pdb=" N ILE A 450 " --> pdb=" O LYS A 490 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 622 through 624 removed outlier: 4.010A pdb=" N SER A 607 " --> pdb=" O GLN A 629 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 622 through 624 removed outlier: 5.757A pdb=" N PHE A 590 " --> pdb=" O SER A 614 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR A 664 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP A 666 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL A 595 " --> pdb=" O ASP A 666 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TRP A 766 " --> pdb=" O TYR A 701 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL A 703 " --> pdb=" O VAL A 764 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N VAL A 764 " --> pdb=" O VAL A 703 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLN A 705 " --> pdb=" O TYR A 762 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N TYR A 762 " --> pdb=" O GLN A 705 " (cutoff:3.500A) 249 hydrogen bonds defined for protein. 705 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.01 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2020 1.34 - 1.45: 980 1.45 - 1.57: 3720 1.57 - 1.69: 15 1.69 - 1.81: 58 Bond restraints: 6793 Sorted by residual: bond pdb=" N VAL A 152 " pdb=" CA VAL A 152 " ideal model delta sigma weight residual 1.465 1.494 -0.030 1.02e-02 9.61e+03 8.37e+00 bond pdb=" N ILE A 150 " pdb=" CA ILE A 150 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.23e-02 6.61e+03 7.15e+00 bond pdb=" N GLU A 680 " pdb=" CA GLU A 680 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.35e+00 bond pdb=" N TYR A 679 " pdb=" CA TYR A 679 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.16e-02 7.43e+03 5.91e+00 bond pdb=" N GLN A 149 " pdb=" CA GLN A 149 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.54e+00 ... (remaining 6788 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 8914 1.30 - 2.60: 265 2.60 - 3.89: 53 3.89 - 5.19: 6 5.19 - 6.49: 4 Bond angle restraints: 9242 Sorted by residual: angle pdb=" CA GLU A 680 " pdb=" C GLU A 680 " pdb=" O GLU A 680 " ideal model delta sigma weight residual 120.82 117.76 3.06 1.05e+00 9.07e-01 8.47e+00 angle pdb=" O5' A B 6 " pdb=" C5' A B 6 " pdb=" C4' A B 6 " ideal model delta sigma weight residual 109.40 111.63 -2.23 8.00e-01 1.56e+00 7.78e+00 angle pdb=" O5' A B 1 " pdb=" C5' A B 1 " pdb=" C4' A B 1 " ideal model delta sigma weight residual 109.40 111.60 -2.20 8.00e-01 1.56e+00 7.54e+00 angle pdb=" CA PRO A 151 " pdb=" C PRO A 151 " pdb=" O PRO A 151 " ideal model delta sigma weight residual 121.95 118.52 3.43 1.25e+00 6.40e-01 7.53e+00 angle pdb=" N LEU A 673 " pdb=" CA LEU A 673 " pdb=" C LEU A 673 " ideal model delta sigma weight residual 109.81 115.55 -5.74 2.21e+00 2.05e-01 6.75e+00 ... (remaining 9237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 3670 17.15 - 34.31: 367 34.31 - 51.46: 54 51.46 - 68.61: 14 68.61 - 85.77: 7 Dihedral angle restraints: 4112 sinusoidal: 1767 harmonic: 2345 Sorted by residual: dihedral pdb=" CA LEU A 133 " pdb=" C LEU A 133 " pdb=" N ALA A 134 " pdb=" CA ALA A 134 " ideal model delta harmonic sigma weight residual 180.00 161.13 18.87 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CB GLU A 670 " pdb=" CG GLU A 670 " pdb=" CD GLU A 670 " pdb=" OE1 GLU A 670 " ideal model delta sinusoidal sigma weight residual 0.00 -85.56 85.56 1 3.00e+01 1.11e-03 9.84e+00 dihedral pdb=" CA CYS A 452 " pdb=" C CYS A 452 " pdb=" N PHE A 453 " pdb=" CA PHE A 453 " ideal model delta harmonic sigma weight residual 180.00 -164.43 -15.57 0 5.00e+00 4.00e-02 9.70e+00 ... (remaining 4109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 696 0.037 - 0.074: 198 0.074 - 0.111: 89 0.111 - 0.148: 33 0.148 - 0.184: 2 Chirality restraints: 1018 Sorted by residual: chirality pdb=" CA ILE A 150 " pdb=" N ILE A 150 " pdb=" C ILE A 150 " pdb=" CB ILE A 150 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.50e-01 chirality pdb=" CB ILE A 237 " pdb=" CA ILE A 237 " pdb=" CG1 ILE A 237 " pdb=" CG2 ILE A 237 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.54e-01 chirality pdb=" CA VAL A 152 " pdb=" N VAL A 152 " pdb=" C VAL A 152 " pdb=" CB VAL A 152 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 1015 not shown) Planarity restraints: 1163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 225 " -0.042 5.00e-02 4.00e+02 6.33e-02 6.40e+00 pdb=" N PRO A 226 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 226 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 226 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 796 " 0.036 5.00e-02 4.00e+02 5.47e-02 4.79e+00 pdb=" N PRO A 797 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 797 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 797 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 181 " -0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO A 182 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 182 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 182 " -0.024 5.00e-02 4.00e+02 ... (remaining 1160 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 408 2.74 - 3.28: 6026 3.28 - 3.82: 9646 3.82 - 4.36: 10735 4.36 - 4.90: 19449 Nonbonded interactions: 46264 Sorted by model distance: nonbonded pdb=" OD1 ASP A 58 " pdb=" OG SER A 129 " model vdw 2.196 3.040 nonbonded pdb=" O TYR A 42 " pdb=" OG1 THR A 403 " model vdw 2.250 3.040 nonbonded pdb=" ND1 HIS A 739 " pdb=" OE1 GLU A 742 " model vdw 2.269 3.120 nonbonded pdb=" O VAL A 175 " pdb=" OG SER A 178 " model vdw 2.299 3.040 nonbonded pdb=" NE2 HIS A 597 " pdb=" OE2 GLU A 634 " model vdw 2.310 3.120 ... (remaining 46259 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: 10.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.720 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 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 : 0.003 0.033 6793 Z= 0.147 Angle : 0.539 6.490 9242 Z= 0.301 Chirality : 0.045 0.184 1018 Planarity : 0.004 0.063 1163 Dihedral : 13.850 85.765 2600 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.28 % Allowed : 0.43 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.50 (0.31), residues: 793 helix: 1.51 (0.34), residues: 257 sheet: -0.63 (0.43), residues: 159 loop : -1.53 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 193 TYR 0.021 0.001 TYR A 801 PHE 0.010 0.001 PHE A 741 TRP 0.005 0.001 TRP A 432 HIS 0.004 0.001 HIS A 761 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.15 ( 6793) covalent geometry : angle 0.53944 / 0.30 ( 9242) hydrogen bonds : bond 0.20015 / 13.19 ( 247) hydrogen bonds : angle 6.62278 / 5.00 ( 705) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 0.157 Fit side-chains REVERT: A 29 ILE cc_start: 0.7942 (mm) cc_final: 0.7720 (mm) REVERT: A 71 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7412 (mt-10) REVERT: A 258 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7896 (mm-30) REVERT: A 263 LYS cc_start: 0.6966 (mmtp) cc_final: 0.6472 (mmtm) REVERT: A 450 ILE cc_start: 0.8402 (mt) cc_final: 0.8134 (tt) REVERT: A 634 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6951 (mm-30) REVERT: A 686 ASP cc_start: 0.8439 (t70) cc_final: 0.8022 (t0) outliers start: 2 outliers final: 0 residues processed: 133 average time/residue: 0.1023 time to fit residues: 17.3930 Evaluate side-chains 78 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.0010 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 HIS A 386 ASN A 761 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.167069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.119923 restraints weight = 8463.099| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 3.27 r_work: 0.3210 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6793 Z= 0.168 Angle : 0.613 8.187 9242 Z= 0.323 Chirality : 0.046 0.174 1018 Planarity : 0.006 0.066 1163 Dihedral : 6.255 84.797 981 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 1.28 % Allowed : 8.09 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.42 (0.31), residues: 793 helix: 1.46 (0.33), residues: 258 sheet: -0.21 (0.45), residues: 148 loop : -1.57 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 25 TYR 0.017 0.002 TYR A 701 PHE 0.021 0.001 PHE A 741 TRP 0.005 0.001 TRP A 448 HIS 0.004 0.001 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 ( 6793) covalent geometry : angle 0.61264 / 0.32 ( 9242) hydrogen bonds : bond 0.05602 / 3.66 ( 247) hydrogen bonds : angle 5.25381 / 3.84 ( 705) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.255 Fit side-chains REVERT: A 71 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7477 (mt-10) REVERT: A 185 TYR cc_start: 0.6840 (m-10) cc_final: 0.6280 (m-80) REVERT: A 258 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7913 (mm-30) REVERT: A 263 LYS cc_start: 0.7128 (mmtp) cc_final: 0.6609 (mmtm) REVERT: A 686 ASP cc_start: 0.8408 (t70) cc_final: 0.7930 (t0) outliers start: 9 outliers final: 8 residues processed: 91 average time/residue: 0.0802 time to fit residues: 9.9560 Evaluate side-chains 86 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LYS Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 459 CYS Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 727 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.167280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.116032 restraints weight = 8419.853| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.96 r_work: 0.3119 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6793 Z= 0.147 Angle : 0.559 6.384 9242 Z= 0.293 Chirality : 0.045 0.176 1018 Planarity : 0.005 0.065 1163 Dihedral : 6.207 86.357 981 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.27 % Allowed : 11.63 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.34 (0.31), residues: 793 helix: 1.57 (0.34), residues: 258 sheet: -0.12 (0.44), residues: 148 loop : -1.58 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 88 TYR 0.011 0.001 TYR A 812 PHE 0.008 0.001 PHE A 199 TRP 0.015 0.001 TRP A 448 HIS 0.006 0.001 HIS A 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 6793) covalent geometry : angle 0.55877 / 0.29 ( 9242) hydrogen bonds : bond 0.05585 / 3.69 ( 247) hydrogen bonds : angle 4.96902 / 3.59 ( 705) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.279 Fit side-chains REVERT: A 71 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7491 (mt-10) REVERT: A 185 TYR cc_start: 0.6992 (m-10) cc_final: 0.6462 (m-80) REVERT: A 263 LYS cc_start: 0.7137 (mmtp) cc_final: 0.6610 (mmtm) REVERT: A 272 MET cc_start: 0.6646 (tmm) cc_final: 0.6410 (tmm) REVERT: A 496 ASP cc_start: 0.7965 (t0) cc_final: 0.7593 (t0) REVERT: A 686 ASP cc_start: 0.8304 (t70) cc_final: 0.7881 (t0) outliers start: 16 outliers final: 13 residues processed: 96 average time/residue: 0.0960 time to fit residues: 12.2193 Evaluate side-chains 83 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LYS Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 459 CYS Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 801 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 7 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 0.0000 chunk 51 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.166305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.114956 restraints weight = 8479.864| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.99 r_work: 0.3175 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6793 Z= 0.142 Angle : 0.556 7.442 9242 Z= 0.289 Chirality : 0.045 0.159 1018 Planarity : 0.005 0.064 1163 Dihedral : 6.187 86.027 981 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 3.26 % Allowed : 12.48 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.31 (0.31), residues: 793 helix: 1.64 (0.33), residues: 258 sheet: -0.23 (0.42), residues: 158 loop : -1.56 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 110 TYR 0.014 0.001 TYR A 701 PHE 0.011 0.001 PHE A 80 TRP 0.006 0.001 TRP A 448 HIS 0.005 0.001 HIS A 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 6793) covalent geometry : angle 0.55615 / 0.29 ( 9242) hydrogen bonds : bond 0.05146 / 3.39 ( 247) hydrogen bonds : angle 4.90880 / 3.54 ( 705) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.265 Fit side-chains REVERT: A 71 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7527 (mt-10) REVERT: A 185 TYR cc_start: 0.7068 (m-10) cc_final: 0.6563 (m-80) REVERT: A 263 LYS cc_start: 0.7209 (mmtp) cc_final: 0.6677 (mmtm) REVERT: A 272 MET cc_start: 0.6576 (tmm) cc_final: 0.6272 (tmm) REVERT: A 496 ASP cc_start: 0.8034 (t0) cc_final: 0.7666 (t0) REVERT: A 615 MET cc_start: 0.8181 (mtt) cc_final: 0.7858 (mtt) REVERT: A 686 ASP cc_start: 0.8335 (t70) cc_final: 0.7917 (t0) outliers start: 23 outliers final: 16 residues processed: 93 average time/residue: 0.0819 time to fit residues: 10.4012 Evaluate side-chains 90 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 127 LYS Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 459 CYS Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 801 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 5 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.0770 chunk 18 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 HIS A 201 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.167213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.115867 restraints weight = 8563.787| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.98 r_work: 0.3195 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6793 Z= 0.117 Angle : 0.522 7.667 9242 Z= 0.272 Chirality : 0.044 0.153 1018 Planarity : 0.005 0.062 1163 Dihedral : 6.077 85.848 981 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.55 % Allowed : 14.89 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.18 (0.31), residues: 793 helix: 1.77 (0.34), residues: 258 sheet: -0.03 (0.44), residues: 150 loop : -1.53 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 110 TYR 0.008 0.001 TYR A 701 PHE 0.007 0.001 PHE A 80 TRP 0.006 0.001 TRP A 448 HIS 0.005 0.001 HIS A 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 6793) covalent geometry : angle 0.52223 / 0.27 ( 9242) hydrogen bonds : bond 0.04505 / 2.96 ( 247) hydrogen bonds : angle 4.81311 / 3.46 ( 705) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.288 Fit side-chains REVERT: A 71 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7528 (mt-10) REVERT: A 185 TYR cc_start: 0.7089 (m-10) cc_final: 0.6605 (m-80) REVERT: A 258 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7442 (mm-30) REVERT: A 263 LYS cc_start: 0.7214 (mmtp) cc_final: 0.6683 (mmtm) REVERT: A 272 MET cc_start: 0.6634 (tmm) cc_final: 0.6259 (tmm) REVERT: A 496 ASP cc_start: 0.8041 (t0) cc_final: 0.7683 (t0) REVERT: A 686 ASP cc_start: 0.8289 (t70) cc_final: 0.7884 (t0) REVERT: A 734 ASP cc_start: 0.7629 (t0) cc_final: 0.7317 (t0) outliers start: 18 outliers final: 16 residues processed: 89 average time/residue: 0.0818 time to fit residues: 9.9901 Evaluate side-chains 88 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 801 TYR Chi-restraints excluded: chain A residue 850 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 15 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 22 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 HIS A 79 HIS A 201 GLN A 597 HIS A 750 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.160708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.109656 restraints weight = 8524.947| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.90 r_work: 0.3041 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 6793 Z= 0.229 Angle : 0.641 6.702 9242 Z= 0.335 Chirality : 0.048 0.172 1018 Planarity : 0.006 0.064 1163 Dihedral : 6.481 86.850 981 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 3.26 % Allowed : 15.18 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.47 (0.31), residues: 793 helix: 1.48 (0.33), residues: 258 sheet: -0.33 (0.41), residues: 167 loop : -1.65 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 110 TYR 0.019 0.002 TYR A 812 PHE 0.015 0.002 PHE A 199 TRP 0.004 0.001 TRP A 196 HIS 0.007 0.001 HIS A 678 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.23 ( 6793) covalent geometry : angle 0.64120 / 0.33 ( 9242) hydrogen bonds : bond 0.07545 / 5.03 ( 247) hydrogen bonds : angle 5.11430 / 3.69 ( 705) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.249 Fit side-chains REVERT: A 71 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7526 (mt-10) REVERT: A 185 TYR cc_start: 0.7223 (m-10) cc_final: 0.6759 (m-80) REVERT: A 263 LYS cc_start: 0.7245 (mmtp) cc_final: 0.6697 (mmtm) REVERT: A 272 MET cc_start: 0.6607 (tmm) cc_final: 0.6160 (tmm) REVERT: A 496 ASP cc_start: 0.8184 (t0) cc_final: 0.7866 (t0) REVERT: A 634 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7650 (mm-30) REVERT: A 686 ASP cc_start: 0.8382 (t70) cc_final: 0.7990 (t0) REVERT: A 734 ASP cc_start: 0.7782 (t0) cc_final: 0.7469 (t0) outliers start: 23 outliers final: 21 residues processed: 91 average time/residue: 0.0753 time to fit residues: 9.5298 Evaluate side-chains 90 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 459 CYS Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 801 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 68 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.164964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.116587 restraints weight = 8359.633| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 3.24 r_work: 0.3179 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6793 Z= 0.118 Angle : 0.538 8.708 9242 Z= 0.281 Chirality : 0.044 0.150 1018 Planarity : 0.005 0.062 1163 Dihedral : 6.217 86.538 981 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.98 % Allowed : 16.03 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.31 (0.31), residues: 793 helix: 1.67 (0.34), residues: 258 sheet: -0.27 (0.41), residues: 167 loop : -1.59 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 110 TYR 0.015 0.001 TYR A 75 PHE 0.007 0.001 PHE A 80 TRP 0.006 0.001 TRP A 448 HIS 0.004 0.001 HIS A 678 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 6793) covalent geometry : angle 0.53830 / 0.28 ( 9242) hydrogen bonds : bond 0.04966 / 3.25 ( 247) hydrogen bonds : angle 4.89547 / 3.52 ( 705) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.266 Fit side-chains REVERT: A 71 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7556 (mt-10) REVERT: A 96 LYS cc_start: 0.7688 (tppt) cc_final: 0.7050 (ttpt) REVERT: A 110 ARG cc_start: 0.6660 (ttp80) cc_final: 0.6437 (ttp80) REVERT: A 185 TYR cc_start: 0.7203 (m-10) cc_final: 0.6777 (m-80) REVERT: A 263 LYS cc_start: 0.7250 (mmtp) cc_final: 0.6718 (mmtm) REVERT: A 496 ASP cc_start: 0.8120 (t0) cc_final: 0.7809 (t0) REVERT: A 634 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7543 (mm-30) REVERT: A 686 ASP cc_start: 0.8338 (t70) cc_final: 0.7994 (t0) REVERT: A 734 ASP cc_start: 0.7669 (t0) cc_final: 0.7397 (t0) REVERT: A 742 GLU cc_start: 0.7165 (mp0) cc_final: 0.6854 (mp0) outliers start: 21 outliers final: 19 residues processed: 93 average time/residue: 0.0762 time to fit residues: 9.7779 Evaluate side-chains 92 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 459 CYS Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 801 TYR Chi-restraints excluded: chain A residue 850 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 14 optimal weight: 8.9990 chunk 10 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 43 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 HIS A 201 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.166190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.115010 restraints weight = 8460.849| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.94 r_work: 0.3185 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6793 Z= 0.115 Angle : 0.525 8.452 9242 Z= 0.271 Chirality : 0.043 0.157 1018 Planarity : 0.005 0.062 1163 Dihedral : 6.090 86.416 981 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 2.55 % Allowed : 16.88 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.25 (0.31), residues: 793 helix: 1.74 (0.34), residues: 258 sheet: -0.13 (0.44), residues: 149 loop : -1.57 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 110 TYR 0.018 0.001 TYR A 75 PHE 0.007 0.001 PHE A 199 TRP 0.006 0.001 TRP A 448 HIS 0.004 0.001 HIS A 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 ( 6793) covalent geometry : angle 0.52484 / 0.27 ( 9242) hydrogen bonds : bond 0.04506 / 2.95 ( 247) hydrogen bonds : angle 4.80399 / 3.45 ( 705) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.192 Fit side-chains REVERT: A 71 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7563 (mt-10) REVERT: A 96 LYS cc_start: 0.7690 (tppt) cc_final: 0.7060 (ttpt) REVERT: A 185 TYR cc_start: 0.7189 (m-10) cc_final: 0.6774 (m-80) REVERT: A 263 LYS cc_start: 0.7302 (mmtp) cc_final: 0.6742 (mmtm) REVERT: A 272 MET cc_start: 0.6574 (tmm) cc_final: 0.6325 (tmm) REVERT: A 496 ASP cc_start: 0.8136 (t0) cc_final: 0.7824 (t0) REVERT: A 634 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7541 (mm-30) REVERT: A 686 ASP cc_start: 0.8330 (t70) cc_final: 0.7931 (t0) REVERT: A 734 ASP cc_start: 0.7616 (t0) cc_final: 0.7376 (t0) REVERT: A 742 GLU cc_start: 0.7077 (mp0) cc_final: 0.6638 (mp0) outliers start: 18 outliers final: 17 residues processed: 93 average time/residue: 0.0808 time to fit residues: 10.2969 Evaluate side-chains 90 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 801 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 60 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 1 optimal weight: 0.0170 chunk 37 optimal weight: 0.0070 chunk 29 optimal weight: 0.6980 chunk 26 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.167851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.119562 restraints weight = 8485.132| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.34 r_work: 0.3220 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6793 Z= 0.099 Angle : 0.509 8.546 9242 Z= 0.261 Chirality : 0.043 0.150 1018 Planarity : 0.005 0.064 1163 Dihedral : 5.968 86.149 981 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.41 % Allowed : 17.30 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.19 (0.31), residues: 793 helix: 1.81 (0.34), residues: 258 sheet: -0.11 (0.43), residues: 157 loop : -1.58 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 110 TYR 0.008 0.001 TYR A 701 PHE 0.006 0.001 PHE A 80 TRP 0.006 0.001 TRP A 448 HIS 0.005 0.001 HIS A 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 ( 6793) covalent geometry : angle 0.50914 / 0.26 ( 9242) hydrogen bonds : bond 0.03804 / 2.47 ( 247) hydrogen bonds : angle 4.72792 / 3.40 ( 705) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.319 Fit side-chains REVERT: A 71 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7551 (mt-10) REVERT: A 96 LYS cc_start: 0.7633 (tppt) cc_final: 0.7096 (ttpt) REVERT: A 185 TYR cc_start: 0.7164 (m-10) cc_final: 0.6769 (m-80) REVERT: A 263 LYS cc_start: 0.7227 (mmtp) cc_final: 0.6672 (mmtm) REVERT: A 272 MET cc_start: 0.6504 (tmm) cc_final: 0.6224 (tmm) REVERT: A 396 ILE cc_start: 0.7872 (mt) cc_final: 0.7666 (mt) REVERT: A 496 ASP cc_start: 0.8111 (t0) cc_final: 0.7795 (t0) REVERT: A 634 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7532 (mm-30) REVERT: A 686 ASP cc_start: 0.8275 (t70) cc_final: 0.7876 (t0) REVERT: A 734 ASP cc_start: 0.7565 (t0) cc_final: 0.7355 (t0) REVERT: A 742 GLU cc_start: 0.7072 (mp0) cc_final: 0.6684 (mp0) outliers start: 17 outliers final: 13 residues processed: 95 average time/residue: 0.0919 time to fit residues: 11.7204 Evaluate side-chains 88 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 801 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 27 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 28 optimal weight: 0.0070 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.167322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.119022 restraints weight = 8468.607| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 3.25 r_work: 0.3215 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6793 Z= 0.108 Angle : 0.524 11.584 9242 Z= 0.267 Chirality : 0.043 0.155 1018 Planarity : 0.005 0.066 1163 Dihedral : 5.944 86.213 981 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.99 % Allowed : 17.59 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.15 (0.31), residues: 793 helix: 1.85 (0.33), residues: 258 sheet: -0.10 (0.43), residues: 157 loop : -1.54 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 110 TYR 0.018 0.001 TYR A 75 PHE 0.009 0.001 PHE A 199 TRP 0.005 0.001 TRP A 448 HIS 0.004 0.001 HIS A 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 6793) covalent geometry : angle 0.52389 / 0.27 ( 9242) hydrogen bonds : bond 0.04062 / 2.64 ( 247) hydrogen bonds : angle 4.70885 / 3.39 ( 705) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.198 Fit side-chains REVERT: A 71 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7520 (mt-10) REVERT: A 96 LYS cc_start: 0.7755 (tppt) cc_final: 0.7421 (mmtt) REVERT: A 185 TYR cc_start: 0.7175 (m-10) cc_final: 0.6784 (m-80) REVERT: A 263 LYS cc_start: 0.7254 (mmtp) cc_final: 0.6681 (mmtm) REVERT: A 272 MET cc_start: 0.6499 (tmm) cc_final: 0.6217 (tmm) REVERT: A 396 ILE cc_start: 0.7892 (mt) cc_final: 0.7690 (mt) REVERT: A 496 ASP cc_start: 0.8119 (t0) cc_final: 0.7803 (t0) REVERT: A 634 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7536 (mm-30) REVERT: A 686 ASP cc_start: 0.8297 (t70) cc_final: 0.7895 (t0) REVERT: A 742 GLU cc_start: 0.7069 (mp0) cc_final: 0.6692 (mp0) outliers start: 14 outliers final: 14 residues processed: 88 average time/residue: 0.0828 time to fit residues: 9.8859 Evaluate side-chains 88 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 801 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 59 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 HIS A 201 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.162169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.115409 restraints weight = 8394.294| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 3.01 r_work: 0.3124 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6793 Z= 0.204 Angle : 0.625 10.562 9242 Z= 0.321 Chirality : 0.047 0.178 1018 Planarity : 0.005 0.065 1163 Dihedral : 6.273 87.174 981 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 2.41 % Allowed : 17.30 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.31 (0.31), residues: 793 helix: 1.69 (0.34), residues: 258 sheet: -0.31 (0.41), residues: 163 loop : -1.57 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 110 TYR 0.012 0.002 TYR A 701 PHE 0.014 0.001 PHE A 199 TRP 0.005 0.001 TRP A 132 HIS 0.006 0.001 HIS A 678 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.20 ( 6793) covalent geometry : angle 0.62454 / 0.32 ( 9242) hydrogen bonds : bond 0.06567 / 4.34 ( 247) hydrogen bonds : angle 4.94710 / 3.58 ( 705) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2021.70 seconds wall clock time: 35 minutes 21.43 seconds (2121.43 seconds total)