Starting phenix.real_space_refine on Thu Jul 2 05:06:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q3f_72192/07_2026/9q3f_72192.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q3f_72192/07_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_72192/07_2026/9q3f_72192.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q3f_72192/07_2026/9q3f_72192.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q3f_72192/07_2026/9q3f_72192.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q3f_72192/07_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-dev-6108/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: 1.68, per 1000 atoms: 0.25 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: 0.54 Conformation dependent library (CDL) restraints added in 397.1 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: 0.22 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: 1.28 Time building geometry restraints manager: 0.67 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: 8936 1.30 - 2.60: 250 2.60 - 3.89: 46 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=" 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 angle pdb=" N LEU A 681 " pdb=" CA LEU A 681 " pdb=" C LEU A 681 " ideal model delta sigma weight residual 111.28 108.53 2.75 1.09e+00 8.42e-01 6.34e+00 angle pdb=" CA TYR A 679 " pdb=" C TYR A 679 " pdb=" O TYR A 679 " ideal model delta sigma weight residual 121.07 118.38 2.69 1.10e+00 8.26e-01 5.96e+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: 704 0.037 - 0.074: 198 0.074 - 0.111: 88 0.111 - 0.148: 26 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: 13.120 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: 0.260 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.900 Find NCS groups from input model: 0.030 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: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.540 ------------------------------------------------------------------------------- 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= 0.146 Angle : 0.527 6.490 9242 Z= 0.288 Chirality : 0.044 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 0.00260 / 0.15 ( 6793) covalent geometry : angle 0.52660 / 0.29 ( 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 : 0.264 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: 0.1050 time to fit residues: 17.8581 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 : 0.258 ------------------------------------------------------------------------------- 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 = 0.3919 r_free = 0.3919 target = 0.166505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.119841 restraints weight = 8401.939| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 3.21 r_work: 0.3143 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6793 Z= 0.172 Angle : 0.622 8.576 9242 Z= 0.328 Chirality : 0.046 0.175 1018 Planarity : 0.006 0.066 1163 Dihedral : 6.269 84.835 981 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 1.42 % Allowed : 7.80 % Favored : 90.78 % 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: -0.43 (0.31), residues: 793 helix: 1.46 (0.33), residues: 258 sheet: -0.22 (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 277 TYR 0.016 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 0.00389 / 0.17 ( 6793) covalent geometry : angle 0.62220 / 0.33 ( 9242) hydrogen bonds : bond 0.05414 / 3.54 ( 247) hydrogen bonds : angle 5.24361 / 3.83 ( 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 95 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.260 Fit side-chains REVERT: A 71 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7477 (mt-10) REVERT: A 185 TYR cc_start: 0.6833 (m-10) cc_final: 0.6269 (m-80) REVERT: A 258 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7919 (mm-30) REVERT: A 263 LYS cc_start: 0.7093 (mmtp) cc_final: 0.6572 (mmtm) REVERT: A 686 ASP cc_start: 0.8387 (t70) cc_final: 0.7912 (t0) outliers start: 10 outliers final: 7 residues processed: 91 average time/residue: 0.0812 time to fit residues: 10.0042 Evaluate side-chains 85 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 35 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 HIS ** A 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.162601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.111449 restraints weight = 8454.540| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.93 r_work: 0.3030 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 6793 Z= 0.229 Angle : 0.650 6.983 9242 Z= 0.342 Chirality : 0.048 0.168 1018 Planarity : 0.006 0.068 1163 Dihedral : 6.538 86.705 981 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 3.26 % Allowed : 12.20 % Favored : 84.54 % 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: -0.59 (0.31), residues: 793 helix: 1.29 (0.33), residues: 258 sheet: -0.36 (0.43), residues: 157 loop : -1.65 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 274 TYR 0.020 0.002 TYR A 812 PHE 0.014 0.002 PHE A 199 TRP 0.012 0.001 TRP A 448 HIS 0.007 0.002 HIS A 739 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.23 ( 6793) covalent geometry : angle 0.65015 / 0.34 ( 9242) hydrogen bonds : bond 0.07653 / 5.09 ( 247) hydrogen bonds : angle 5.23122 / 3.78 ( 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 101 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 0.276 Fit side-chains REVERT: A 71 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7512 (mt-10) REVERT: A 185 TYR cc_start: 0.7123 (m-10) cc_final: 0.6618 (m-80) REVERT: A 263 LYS cc_start: 0.7178 (mmtp) cc_final: 0.6651 (mmtm) REVERT: A 272 MET cc_start: 0.6638 (tmm) cc_final: 0.6366 (tmm) REVERT: A 496 ASP cc_start: 0.8074 (t0) cc_final: 0.7735 (t0) REVERT: A 686 ASP cc_start: 0.8379 (t70) cc_final: 0.7966 (t0) outliers start: 23 outliers final: 18 residues processed: 94 average time/residue: 0.0937 time to fit residues: 11.6308 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 : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 164 MET 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 379 LEU 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 7 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 44 optimal weight: 0.0040 chunk 69 optimal weight: 0.3980 chunk 52 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 overall best weight: 1.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 HIS ** A 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.165671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.114217 restraints weight = 8456.389| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.97 r_work: 0.3094 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6793 Z= 0.128 Angle : 0.556 8.063 9242 Z= 0.291 Chirality : 0.044 0.152 1018 Planarity : 0.005 0.063 1163 Dihedral : 6.294 85.700 981 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.13 % Allowed : 14.47 % Favored : 83.40 % 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: -0.39 (0.31), residues: 793 helix: 1.55 (0.33), residues: 258 sheet: -0.25 (0.42), residues: 158 loop : -1.60 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 88 TYR 0.014 0.001 TYR A 75 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 0.00291 / 0.13 ( 6793) covalent geometry : angle 0.55559 / 0.29 ( 9242) hydrogen bonds : bond 0.05095 / 3.35 ( 247) hydrogen bonds : angle 4.97795 / 3.59 ( 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 92 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.266 Fit side-chains REVERT: A 71 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7517 (mt-10) REVERT: A 127 LYS cc_start: 0.5931 (OUTLIER) cc_final: 0.5610 (ptmt) REVERT: A 185 TYR cc_start: 0.7099 (m-10) cc_final: 0.6601 (m-80) REVERT: A 263 LYS cc_start: 0.7185 (mmtp) cc_final: 0.6664 (mmtm) REVERT: A 272 MET cc_start: 0.6554 (tmm) cc_final: 0.6221 (tmm) REVERT: A 496 ASP cc_start: 0.8047 (t0) cc_final: 0.7713 (t0) REVERT: A 686 ASP cc_start: 0.8297 (t70) cc_final: 0.7905 (t0) outliers start: 15 outliers final: 11 residues processed: 89 average time/residue: 0.0833 time to fit residues: 10.1678 Evaluate side-chains 86 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 160 LEU 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 588 VAL Chi-restraints excluded: chain A residue 721 ILE 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: 0.6980 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 HIS A 750 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.165623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.114543 restraints weight = 8516.080| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.95 r_work: 0.3102 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6793 Z= 0.132 Angle : 0.533 6.294 9242 Z= 0.281 Chirality : 0.044 0.157 1018 Planarity : 0.005 0.064 1163 Dihedral : 6.196 85.698 981 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 2.70 % Allowed : 15.04 % Favored : 82.27 % 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: -0.30 (0.31), residues: 793 helix: 1.61 (0.33), residues: 258 sheet: -0.12 (0.44), residues: 148 loop : -1.54 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 110 TYR 0.010 0.001 TYR A 701 PHE 0.013 0.001 PHE A 80 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 0.00303 / 0.13 ( 6793) covalent geometry : angle 0.53343 / 0.28 ( 9242) hydrogen bonds : bond 0.05014 / 3.32 ( 247) hydrogen bonds : angle 4.88199 / 3.51 ( 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 93 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.266 Fit side-chains REVERT: A 71 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7543 (mt-10) REVERT: A 127 LYS cc_start: 0.5844 (OUTLIER) cc_final: 0.5501 (ptmt) REVERT: A 185 TYR cc_start: 0.7142 (m-10) cc_final: 0.6645 (m-80) REVERT: A 263 LYS cc_start: 0.7218 (mmtp) cc_final: 0.6692 (mmtm) REVERT: A 272 MET cc_start: 0.6594 (tmm) cc_final: 0.6215 (tmm) REVERT: A 496 ASP cc_start: 0.8087 (t0) cc_final: 0.7755 (t0) REVERT: A 686 ASP cc_start: 0.8281 (t70) cc_final: 0.7896 (t0) REVERT: A 734 ASP cc_start: 0.7702 (t0) cc_final: 0.7382 (t0) REVERT: A 742 GLU cc_start: 0.7184 (mp0) cc_final: 0.6750 (mp0) outliers start: 19 outliers final: 16 residues processed: 91 average time/residue: 0.0777 time to fit residues: 9.8120 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 : 0.267 ------------------------------------------------------------------------------- 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 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 379 LEU 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 727 ILE 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: 7.9990 chunk 70 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 17 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 22 optimal weight: 0.0770 chunk 47 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 overall best weight: 1.2944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 HIS A 597 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.164877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.113463 restraints weight = 8522.041| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.97 r_work: 0.3088 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6793 Z= 0.138 Angle : 0.542 8.319 9242 Z= 0.282 Chirality : 0.044 0.156 1018 Planarity : 0.005 0.066 1163 Dihedral : 6.176 85.805 981 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.12 % Allowed : 15.60 % Favored : 81.28 % 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: -0.26 (0.31), residues: 793 helix: 1.67 (0.34), residues: 258 sheet: -0.15 (0.43), residues: 159 loop : -1.55 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 110 TYR 0.016 0.001 TYR A 75 PHE 0.008 0.001 PHE A 199 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 0.00323 / 0.14 ( 6793) covalent geometry : angle 0.54228 / 0.28 ( 9242) hydrogen bonds : bond 0.05153 / 3.40 ( 247) hydrogen bonds : angle 4.87607 / 3.52 ( 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 95 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.345 Fit side-chains REVERT: A 71 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7552 (mt-10) REVERT: A 110 ARG cc_start: 0.6650 (ttp80) cc_final: 0.6425 (ttp80) REVERT: A 127 LYS cc_start: 0.5888 (OUTLIER) cc_final: 0.5533 (ptmt) REVERT: A 185 TYR cc_start: 0.7144 (m-10) cc_final: 0.6673 (m-80) REVERT: A 263 LYS cc_start: 0.7233 (mmtp) cc_final: 0.6693 (mmtm) REVERT: A 272 MET cc_start: 0.6532 (tmm) cc_final: 0.6133 (tmm) REVERT: A 496 ASP cc_start: 0.8109 (t0) cc_final: 0.7790 (t0) REVERT: A 634 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7643 (mm-30) REVERT: A 686 ASP cc_start: 0.8280 (t70) cc_final: 0.7895 (t0) REVERT: A 734 ASP cc_start: 0.7694 (t0) cc_final: 0.7383 (t0) outliers start: 22 outliers final: 21 residues processed: 93 average time/residue: 0.0778 time to fit residues: 10.0152 Evaluate side-chains 94 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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 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 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 588 VAL Chi-restraints excluded: chain A residue 612 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: 0.9980 chunk 30 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 45 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.166825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.115744 restraints weight = 8399.615| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.93 r_work: 0.3198 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6793 Z= 0.111 Angle : 0.517 8.245 9242 Z= 0.268 Chirality : 0.043 0.153 1018 Planarity : 0.005 0.061 1163 Dihedral : 6.045 85.746 981 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.27 % Allowed : 17.16 % 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: -0.19 (0.31), residues: 793 helix: 1.75 (0.34), residues: 258 sheet: -0.02 (0.45), residues: 150 loop : -1.55 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 110 TYR 0.016 0.001 TYR A 75 PHE 0.009 0.001 PHE A 80 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 0.00250 / 0.11 ( 6793) covalent geometry : angle 0.51662 / 0.27 ( 9242) hydrogen bonds : bond 0.04356 / 2.84 ( 247) hydrogen bonds : angle 4.79389 / 3.44 ( 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 92 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.268 Fit side-chains REVERT: A 71 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7554 (mt-10) REVERT: A 127 LYS cc_start: 0.5944 (OUTLIER) cc_final: 0.5576 (ptmt) REVERT: A 185 TYR cc_start: 0.7167 (m-10) cc_final: 0.6747 (m-80) REVERT: A 263 LYS cc_start: 0.7288 (mmtp) cc_final: 0.6739 (mmtm) REVERT: A 272 MET cc_start: 0.6571 (tmm) cc_final: 0.6281 (tmm) REVERT: A 496 ASP cc_start: 0.8104 (t0) cc_final: 0.7782 (t0) REVERT: A 634 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7559 (mm-30) REVERT: A 686 ASP cc_start: 0.8330 (t70) cc_final: 0.7981 (t0) REVERT: A 734 ASP cc_start: 0.7618 (t0) cc_final: 0.7359 (t0) REVERT: A 742 GLU cc_start: 0.7045 (mp0) cc_final: 0.6828 (mp0) outliers start: 16 outliers final: 15 residues processed: 91 average time/residue: 0.0791 time to fit residues: 9.9215 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 : 0.265 ------------------------------------------------------------------------------- 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 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 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 772 THR Chi-restraints excluded: chain A residue 801 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 58 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 65 optimal weight: 0.0770 chunk 75 optimal weight: 0.0770 chunk 19 optimal weight: 2.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- 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 = 0.3930 r_free = 0.3930 target = 0.167339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.116635 restraints weight = 8429.036| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.93 r_work: 0.3209 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3938 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= 0.107 Angle : 0.513 8.542 9242 Z= 0.265 Chirality : 0.043 0.153 1018 Planarity : 0.005 0.062 1163 Dihedral : 5.981 85.645 981 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.41 % Allowed : 17.59 % Favored : 80.00 % 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: -0.14 (0.31), residues: 793 helix: 1.80 (0.33), residues: 258 sheet: -0.05 (0.43), residues: 160 loop : -1.52 (0.32), residues: 375 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 0.006 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 0.00237 / 0.11 ( 6793) covalent geometry : angle 0.51313 / 0.26 ( 9242) hydrogen bonds : bond 0.04178 / 2.73 ( 247) hydrogen bonds : angle 4.73021 / 3.41 ( 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 93 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.227 Fit side-chains REVERT: A 71 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7557 (mt-10) REVERT: A 96 LYS cc_start: 0.7681 (tppt) cc_final: 0.7144 (ttpt) REVERT: A 127 LYS cc_start: 0.5956 (OUTLIER) cc_final: 0.5557 (ptmt) REVERT: A 185 TYR cc_start: 0.7159 (m-10) cc_final: 0.6753 (m-80) REVERT: A 263 LYS cc_start: 0.7310 (mmtp) cc_final: 0.6758 (mmtm) REVERT: A 496 ASP cc_start: 0.8108 (t0) cc_final: 0.7785 (t0) REVERT: A 634 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7540 (mm-30) REVERT: A 686 ASP cc_start: 0.8319 (t70) cc_final: 0.7928 (t0) REVERT: A 734 ASP cc_start: 0.7577 (t0) cc_final: 0.7337 (t0) REVERT: A 742 GLU cc_start: 0.6981 (mp0) cc_final: 0.6604 (mp0) outliers start: 17 outliers final: 15 residues processed: 92 average time/residue: 0.0874 time to fit residues: 10.7349 Evaluate side-chains 89 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain A residue 850 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 60 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 chunk 64 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3929 r_free = 0.3929 target = 0.167025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.115775 restraints weight = 8517.594| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.96 r_work: 0.3200 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.4022 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= 0.111 Angle : 0.520 9.242 9242 Z= 0.266 Chirality : 0.043 0.155 1018 Planarity : 0.005 0.064 1163 Dihedral : 5.960 85.774 981 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.27 % Allowed : 17.59 % Favored : 80.14 % 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: -0.12 (0.31), residues: 793 helix: 1.83 (0.33), residues: 258 sheet: 0.01 (0.44), residues: 154 loop : -1.52 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 110 TYR 0.017 0.001 TYR A 75 PHE 0.006 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 0.00253 / 0.11 ( 6793) covalent geometry : angle 0.51985 / 0.27 ( 9242) hydrogen bonds : bond 0.04255 / 2.77 ( 247) hydrogen bonds : angle 4.71655 / 3.39 ( 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 90 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.274 Fit side-chains REVERT: A 71 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7557 (mt-10) REVERT: A 96 LYS cc_start: 0.7731 (tppt) cc_final: 0.7089 (ttpt) REVERT: A 127 LYS cc_start: 0.5911 (OUTLIER) cc_final: 0.5511 (ptmt) REVERT: A 185 TYR cc_start: 0.7146 (m-10) cc_final: 0.6739 (m-80) REVERT: A 263 LYS cc_start: 0.7268 (mmtp) cc_final: 0.6724 (mmtm) REVERT: A 272 MET cc_start: 0.6542 (tmm) cc_final: 0.6286 (tmm) REVERT: A 422 ARG cc_start: 0.7769 (mmp80) cc_final: 0.7490 (mmp-170) REVERT: A 496 ASP cc_start: 0.8116 (t0) cc_final: 0.7795 (t0) REVERT: A 634 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7551 (mm-30) REVERT: A 686 ASP cc_start: 0.8287 (t70) cc_final: 0.7889 (t0) REVERT: A 734 ASP cc_start: 0.7566 (t0) cc_final: 0.7331 (t0) REVERT: A 742 GLU cc_start: 0.6959 (mp0) cc_final: 0.6550 (mp0) outliers start: 16 outliers final: 15 residues processed: 89 average time/residue: 0.0834 time to fit residues: 9.9092 Evaluate side-chains 89 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.191 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain A residue 850 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 27 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 48 optimal weight: 0.0040 chunk 64 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 7 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- 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 = 0.3942 r_free = 0.3942 target = 0.168356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.120483 restraints weight = 8403.895| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.24 r_work: 0.3239 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6793 Z= 0.100 Angle : 0.515 12.099 9242 Z= 0.262 Chirality : 0.043 0.151 1018 Planarity : 0.005 0.064 1163 Dihedral : 5.869 85.744 981 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.13 % Allowed : 17.73 % Favored : 80.14 % 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: -0.09 (0.31), residues: 793 helix: 1.89 (0.34), residues: 257 sheet: -0.02 (0.43), residues: 156 loop : -1.52 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 110 TYR 0.008 0.001 TYR A 701 PHE 0.005 0.001 PHE A 745 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 0.00222 / 0.10 ( 6793) covalent geometry : angle 0.51545 / 0.26 ( 9242) hydrogen bonds : bond 0.03707 / 2.40 ( 247) hydrogen bonds : angle 4.67288 / 3.36 ( 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: 15 poor density : 74 time to evaluate : 0.229 Fit side-chains REVERT: A 71 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7514 (mt-10) REVERT: A 96 LYS cc_start: 0.7731 (tppt) cc_final: 0.7399 (mmtt) REVERT: A 127 LYS cc_start: 0.5890 (OUTLIER) cc_final: 0.5490 (ptmt) REVERT: A 185 TYR cc_start: 0.7156 (m-10) cc_final: 0.6776 (m-80) REVERT: A 263 LYS cc_start: 0.7241 (mmtp) cc_final: 0.6686 (mmtm) REVERT: A 272 MET cc_start: 0.6449 (tmm) cc_final: 0.6187 (tmm) REVERT: A 396 ILE cc_start: 0.7888 (mt) cc_final: 0.7687 (mt) REVERT: A 496 ASP cc_start: 0.8092 (t0) cc_final: 0.7765 (t0) REVERT: A 634 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7530 (mm-30) REVERT: A 686 ASP cc_start: 0.8267 (t70) cc_final: 0.7871 (t0) REVERT: A 734 ASP cc_start: 0.7523 (t0) cc_final: 0.7315 (t0) REVERT: A 739 HIS cc_start: 0.7310 (OUTLIER) cc_final: 0.6883 (t-90) REVERT: A 742 GLU cc_start: 0.6900 (mp0) cc_final: 0.6667 (mp0) REVERT: A 801 TYR cc_start: 0.8565 (OUTLIER) cc_final: 0.7990 (m-80) outliers start: 15 outliers final: 12 residues processed: 88 average time/residue: 0.0824 time to fit residues: 9.9759 Evaluate side-chains 86 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.199 ------------------------------------------------------------------------------- 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 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 474 ILE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 739 HIS 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: 2.9990 chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 21 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 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 = 0.3910 r_free = 0.3910 target = 0.165309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.114426 restraints weight = 8350.087| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.91 r_work: 0.3184 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6793 Z= 0.135 Angle : 0.541 10.302 9242 Z= 0.277 Chirality : 0.044 0.162 1018 Planarity : 0.005 0.065 1163 Dihedral : 5.972 86.157 981 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.70 % Allowed : 17.45 % Favored : 79.86 % 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: -0.09 (0.31), residues: 793 helix: 1.84 (0.34), residues: 258 sheet: -0.05 (0.43), residues: 161 loop : -1.48 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 110 TYR 0.017 0.001 TYR A 75 PHE 0.010 0.001 PHE A 199 TRP 0.005 0.001 TRP A 448 HIS 0.004 0.001 HIS A 739 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 6793) covalent geometry : angle 0.54106 / 0.28 ( 9242) hydrogen bonds : bond 0.04966 / 3.24 ( 247) hydrogen bonds : angle 4.75458 / 3.43 ( 705) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2044.56 seconds wall clock time: 35 minutes 46.46 seconds (2146.46 seconds total)