Starting phenix.real_space_refine on Tue Aug 4 12:03:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/30bt_57548/08_2026/30bt_57548.cif Found real_map, /net/cci-nas-00/data/ceres_data/30bt_57548/08_2026/30bt_57548.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/30bt_57548/08_2026/30bt_57548.map" default_real_map = "/net/cci-nas-00/data/ceres_data/30bt_57548/08_2026/30bt_57548.map" model { file = "/net/cci-nas-00/data/ceres_data/30bt_57548/08_2026/30bt_57548.cif" } default_model = "/net/cci-nas-00/data/ceres_data/30bt_57548/08_2026/30bt_57548.cif" } resolution = 4.2 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= 0.013 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: 4 Type Number sf(0) Gaussians S 5 5.16 5 C 1326 2.51 5 N 379 2.21 5 O 387 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2097 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2097 Classifications: {'peptide': 273} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 254} Time building chain proxies: 0.58, per 1000 atoms: 0.28 Number of scatterers: 2097 At special positions: 0 Unit cell: (63.756, 56.672, 58.696, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 5 16.00 O 387 8.00 N 379 7.00 C 1326 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: 0.16 Conformation dependent library (CDL) restraints added in 87.3 milliseconds 542 Ramachandran restraints generated. 271 Oldfield, 0 Emsley, 271 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 486 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 2 sheets defined 34.4% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing helix chain 'A' and resid 574 through 579 Processing helix chain 'A' and resid 579 through 586 Processing helix chain 'A' and resid 600 through 605 removed outlier: 3.849A pdb=" N ILE A 604 " --> pdb=" O ASP A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 614 removed outlier: 3.713A pdb=" N GLU A 613 " --> pdb=" O ALA A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 642 removed outlier: 3.842A pdb=" N ASP A 630 " --> pdb=" O GLY A 626 " (cutoff:3.500A) Proline residue: A 634 - end of helix removed outlier: 3.794A pdb=" N GLU A 638 " --> pdb=" O PRO A 634 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG A 642 " --> pdb=" O GLU A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 681 Processing helix chain 'A' and resid 702 through 713 removed outlier: 3.850A pdb=" N GLY A 713 " --> pdb=" O LEU A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 732 removed outlier: 6.836A pdb=" N ARG A 729 " --> pdb=" O HIS A 726 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N TYR A 730 " --> pdb=" O GLY A 727 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 732 " --> pdb=" O ARG A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 741 Processing helix chain 'A' and resid 759 through 766 removed outlier: 3.531A pdb=" N TRP A 766 " --> pdb=" O ILE A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 780 Processing sheet with id=AA1, first strand: chain 'A' and resid 646 through 648 removed outlier: 3.690A pdb=" N GLN A 647 " --> pdb=" O VAL A 619 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL A 594 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N HIS A 557 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ILE A 595 " --> pdb=" O HIS A 557 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU A 559 " --> pdb=" O ILE A 595 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE A 782 " --> pdb=" O PHE A 539 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.931A pdb=" N ILE A 663 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL A 745 " --> pdb=" O TYR A 774 " (cutoff:3.500A) 67 hydrogen bonds defined for protein. 174 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: 0.26 Time building geometry restraints manager: 0.23 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: 723 1.34 - 1.46: 300 1.46 - 1.57: 1114 1.57 - 1.69: 0 1.69 - 1.80: 10 Bond restraints: 2147 Sorted by residual: bond pdb=" C ILE A 747 " pdb=" O ILE A 747 " ideal model delta sigma weight residual 1.232 1.239 -0.007 1.01e-02 9.80e+03 5.41e-01 bond pdb=" C VAL A 542 " pdb=" N GLY A 543 " ideal model delta sigma weight residual 1.335 1.329 0.006 7.50e-03 1.78e+04 5.39e-01 bond pdb=" CA GLY A 543 " pdb=" C GLY A 543 " ideal model delta sigma weight residual 1.522 1.513 0.009 1.30e-02 5.92e+03 5.17e-01 bond pdb=" C HIS A 598 " pdb=" O HIS A 598 " ideal model delta sigma weight residual 1.244 1.238 0.006 1.10e-02 8.26e+03 2.94e-01 bond pdb=" C HIS A 757 " pdb=" N PRO A 758 " ideal model delta sigma weight residual 1.334 1.346 -0.012 2.34e-02 1.83e+03 2.77e-01 ... (remaining 2142 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 2837 1.04 - 2.08: 63 2.08 - 3.12: 15 3.12 - 4.16: 4 4.16 - 5.20: 3 Bond angle restraints: 2922 Sorted by residual: angle pdb=" CA GLY A 543 " pdb=" C GLY A 543 " pdb=" N GLN A 544 " ideal model delta sigma weight residual 115.64 116.85 -1.21 7.90e-01 1.60e+00 2.33e+00 angle pdb=" C VAL A 746 " pdb=" N ILE A 747 " pdb=" CA ILE A 747 " ideal model delta sigma weight residual 123.25 121.64 1.61 1.10e+00 8.26e-01 2.13e+00 angle pdb=" CA ILE A 747 " pdb=" C ILE A 747 " pdb=" O ILE A 747 " ideal model delta sigma weight residual 120.88 119.97 0.91 6.80e-01 2.16e+00 1.77e+00 angle pdb=" C THR A 597 " pdb=" N HIS A 598 " pdb=" CA HIS A 598 " ideal model delta sigma weight residual 122.65 120.50 2.15 1.66e+00 3.63e-01 1.68e+00 angle pdb=" C HIS A 757 " pdb=" N PRO A 758 " pdb=" CD PRO A 758 " ideal model delta sigma weight residual 125.00 130.20 -5.20 4.10e+00 5.95e-02 1.61e+00 ... (remaining 2917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.15: 1207 14.15 - 28.30: 54 28.30 - 42.45: 11 42.45 - 56.60: 1 56.60 - 70.76: 2 Dihedral angle restraints: 1275 sinusoidal: 509 harmonic: 766 Sorted by residual: dihedral pdb=" N LEU A 607 " pdb=" CA LEU A 607 " pdb=" CB LEU A 607 " pdb=" CG LEU A 607 " ideal model delta sinusoidal sigma weight residual -60.00 -114.97 54.97 3 1.50e+01 4.44e-03 9.32e+00 dihedral pdb=" CB GLU A 751 " pdb=" CG GLU A 751 " pdb=" CD GLU A 751 " pdb=" OE1 GLU A 751 " ideal model delta sinusoidal sigma weight residual 0.00 -70.76 70.76 1 3.00e+01 1.11e-03 7.15e+00 dihedral pdb=" N ARG A 775 " pdb=" CA ARG A 775 " pdb=" CB ARG A 775 " pdb=" CG ARG A 775 " ideal model delta sinusoidal sigma weight residual -180.00 -140.84 -39.16 3 1.50e+01 4.44e-03 6.93e+00 ... (remaining 1272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 177 0.028 - 0.056: 87 0.056 - 0.084: 18 0.084 - 0.112: 30 0.112 - 0.140: 8 Chirality restraints: 320 Sorted by residual: chirality pdb=" CA ILE A 797 " pdb=" N ILE A 797 " pdb=" C ILE A 797 " pdb=" CB ILE A 797 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA VAL A 771 " pdb=" N VAL A 771 " pdb=" C VAL A 771 " pdb=" CB VAL A 771 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.68e-01 chirality pdb=" CA ILE A 595 " pdb=" N ILE A 595 " pdb=" C ILE A 595 " pdb=" CB ILE A 595 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.45e-01 ... (remaining 317 not shown) Planarity restraints: 391 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 644 " 0.018 5.00e-02 4.00e+02 2.74e-02 1.20e+00 pdb=" N PRO A 645 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 645 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 645 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 667 " -0.013 5.00e-02 4.00e+02 2.04e-02 6.65e-01 pdb=" N PRO A 668 " 0.035 5.00e-02 4.00e+02 pdb=" CA PRO A 668 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO A 668 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 757 " 0.013 5.00e-02 4.00e+02 1.98e-02 6.27e-01 pdb=" N PRO A 758 " -0.034 5.00e-02 4.00e+02 pdb=" CA PRO A 758 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO A 758 " 0.011 5.00e-02 4.00e+02 ... (remaining 388 not shown) Histogram of nonbonded interaction distances: 2.68 - 3.12: 1536 3.12 - 3.57: 2137 3.57 - 4.01: 3212 4.01 - 4.46: 3741 4.46 - 4.90: 5900 Nonbonded interactions: 16526 Sorted by model distance: nonbonded pdb=" N SER A 675 " pdb=" O SER A 675 " model vdw 2.678 2.496 nonbonded pdb=" N PHE A 572 " pdb=" O PHE A 572 " model vdw 2.680 2.496 nonbonded pdb=" N GLY A 800 " pdb=" O GLY A 800 " model vdw 2.681 2.496 nonbonded pdb=" N ALA A 699 " pdb=" O ALA A 699 " model vdw 2.681 2.496 nonbonded pdb=" O HIS A 757 " pdb=" CA PRO A 758 " model vdw 2.683 2.776 ... (remaining 16521 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.020 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.940 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2147 Z= 0.094 Angle : 0.447 5.202 2922 Z= 0.234 Chirality : 0.046 0.140 320 Planarity : 0.004 0.027 391 Dihedral : 8.929 70.756 789 Min Nonbonded Distance : 2.678 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.53), residues: 271 helix: 0.15 (0.70), residues: 57 sheet: 1.57 (0.66), residues: 65 loop : 0.44 (0.55), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 589 TYR 0.005 0.001 TYR A 549 PHE 0.006 0.001 PHE A 539 TRP 0.004 0.001 TRP A 766 HIS 0.001 0.000 HIS A 598 Details of bonding type rmsd/Z covalent geometry : bond 0.00174 / 0.09 ( 2147) covalent geometry : angle 0.44681 / 0.23 ( 2922) hydrogen bonds : bond 0.20197 / 14.26 ( 67) hydrogen bonds : angle 8.96720 / 6.24 ( 174) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 542 Ramachandran restraints generated. 271 Oldfield, 0 Emsley, 271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 542 Ramachandran restraints generated. 271 Oldfield, 0 Emsley, 271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 540 ILE cc_start: 0.9064 (mt) cc_final: 0.8780 (mt) REVERT: A 586 GLN cc_start: 0.8456 (mt0) cc_final: 0.8225 (tt0) REVERT: A 598 HIS cc_start: 0.7768 (t70) cc_final: 0.7365 (t-170) REVERT: A 603 HIS cc_start: 0.5727 (m-70) cc_final: 0.3061 (m-70) REVERT: A 680 ASN cc_start: 0.7817 (m-40) cc_final: 0.7575 (m110) REVERT: A 706 MET cc_start: 0.7068 (tpp) cc_final: 0.6738 (ppp) REVERT: A 783 THR cc_start: 0.8455 (m) cc_final: 0.8216 (p) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0547 time to fit residues: 5.4367 Evaluate side-chains 55 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 0.0020 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 26 optimal weight: 0.1980 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 544 GLN A 767 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.186848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.158970 restraints weight = 3988.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.163881 restraints weight = 2729.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.167801 restraints weight = 2029.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.170663 restraints weight = 1591.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.172667 restraints weight = 1291.460| |-----------------------------------------------------------------------------| r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2147 Z= 0.143 Angle : 0.587 6.046 2922 Z= 0.301 Chirality : 0.048 0.145 320 Planarity : 0.006 0.054 391 Dihedral : 3.848 13.353 300 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.51), residues: 271 helix: 0.50 (0.73), residues: 52 sheet: 1.48 (0.65), residues: 60 loop : 0.19 (0.51), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 651 TYR 0.008 0.001 TYR A 774 PHE 0.019 0.002 PHE A 721 TRP 0.006 0.001 TRP A 766 HIS 0.005 0.001 HIS A 598 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 2147) covalent geometry : angle 0.58668 / 0.30 ( 2922) hydrogen bonds : bond 0.03980 / 2.65 ( 67) hydrogen bonds : angle 7.19508 / 4.95 ( 174) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 542 Ramachandran restraints generated. 271 Oldfield, 0 Emsley, 271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 542 Ramachandran restraints generated. 271 Oldfield, 0 Emsley, 271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.043 Fit side-chains revert: symmetry clash REVERT: A 540 ILE cc_start: 0.9191 (mt) cc_final: 0.8885 (mt) REVERT: A 558 ILE cc_start: 0.8708 (mt) cc_final: 0.8481 (mt) REVERT: A 583 LEU cc_start: 0.8089 (mt) cc_final: 0.7779 (mt) REVERT: A 585 ARG cc_start: 0.4619 (tpm170) cc_final: 0.1608 (mtm-85) REVERT: A 586 GLN cc_start: 0.8286 (mt0) cc_final: 0.8006 (tt0) REVERT: A 752 LYS cc_start: 0.8001 (mmmt) cc_final: 0.7719 (mmmt) REVERT: A 763 LEU cc_start: 0.8295 (mt) cc_final: 0.7972 (mt) REVERT: A 768 GLU cc_start: 0.7474 (tt0) cc_final: 0.7216 (mt-10) REVERT: A 783 THR cc_start: 0.8283 (m) cc_final: 0.8034 (p) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.0546 time to fit residues: 4.2363 Evaluate side-chains 51 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 21 optimal weight: 0.3980 chunk 15 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 0.0870 chunk 17 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 0 optimal weight: 0.5980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.185877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.159484 restraints weight = 4177.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.164546 restraints weight = 2822.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.168255 restraints weight = 2077.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.171248 restraints weight = 1611.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.173194 restraints weight = 1287.673| |-----------------------------------------------------------------------------| r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2147 Z= 0.146 Angle : 0.633 9.777 2922 Z= 0.316 Chirality : 0.048 0.136 320 Planarity : 0.005 0.038 391 Dihedral : 4.238 21.814 300 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.50), residues: 271 helix: -0.69 (0.60), residues: 64 sheet: 1.19 (0.65), residues: 60 loop : -0.12 (0.51), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 734 TYR 0.031 0.002 TYR A 765 PHE 0.016 0.002 PHE A 635 TRP 0.004 0.001 TRP A 766 HIS 0.003 0.001 HIS A 603 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 2147) covalent geometry : angle 0.63317 / 0.32 ( 2922) hydrogen bonds : bond 0.03587 / 2.47 ( 67) hydrogen bonds : angle 7.20630 / 4.90 ( 174) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 542 Ramachandran restraints generated. 271 Oldfield, 0 Emsley, 271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 542 Ramachandran restraints generated. 271 Oldfield, 0 Emsley, 271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.044 Fit side-chains REVERT: A 540 ILE cc_start: 0.9231 (mt) cc_final: 0.8943 (mt) REVERT: A 558 ILE cc_start: 0.8760 (mt) cc_final: 0.8513 (mt) REVERT: A 583 LEU cc_start: 0.8138 (mt) cc_final: 0.7834 (mt) REVERT: A 585 ARG cc_start: 0.4730 (tpm170) cc_final: 0.1632 (mtm-85) REVERT: A 586 GLN cc_start: 0.8309 (mt0) cc_final: 0.8058 (tt0) REVERT: A 706 MET cc_start: 0.6330 (ppp) cc_final: 0.6121 (ppp) REVERT: A 752 LYS cc_start: 0.7999 (mmmt) cc_final: 0.7611 (mmmt) REVERT: A 768 GLU cc_start: 0.7611 (tt0) cc_final: 0.7250 (mt-10) REVERT: A 777 ASP cc_start: 0.7311 (p0) cc_final: 0.7099 (p0) REVERT: A 783 THR cc_start: 0.8634 (m) cc_final: 0.8424 (p) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0475 time to fit residues: 3.2887 Evaluate side-chains 48 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 3 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 14 optimal weight: 0.2980 chunk 16 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 603 HIS ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.183579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.157377 restraints weight = 4018.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.162379 restraints weight = 2728.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.166099 restraints weight = 1975.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.168745 restraints weight = 1516.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.170886 restraints weight = 1222.749| |-----------------------------------------------------------------------------| r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2147 Z= 0.148 Angle : 0.603 6.158 2922 Z= 0.302 Chirality : 0.048 0.136 320 Planarity : 0.005 0.039 391 Dihedral : 4.266 17.383 300 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.50), residues: 271 helix: -0.63 (0.62), residues: 58 sheet: 0.93 (0.65), residues: 60 loop : 0.09 (0.52), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 734 TYR 0.019 0.002 TYR A 765 PHE 0.010 0.002 PHE A 721 TRP 0.005 0.001 TRP A 646 HIS 0.003 0.001 HIS A 667 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 2147) covalent geometry : angle 0.60347 / 0.30 ( 2922) hydrogen bonds : bond 0.03296 / 2.22 ( 67) hydrogen bonds : angle 7.05174 / 4.78 ( 174) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 542 Ramachandran restraints generated. 271 Oldfield, 0 Emsley, 271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 542 Ramachandran restraints generated. 271 Oldfield, 0 Emsley, 271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.074 Fit side-chains REVERT: A 540 ILE cc_start: 0.9249 (mt) cc_final: 0.8963 (mt) REVERT: A 558 ILE cc_start: 0.8766 (mt) cc_final: 0.8523 (mt) REVERT: A 583 LEU cc_start: 0.8287 (mt) cc_final: 0.8034 (mt) REVERT: A 585 ARG cc_start: 0.4813 (tpm170) cc_final: 0.1697 (mtm-85) REVERT: A 598 HIS cc_start: 0.7865 (t-170) cc_final: 0.7646 (t-170) REVERT: A 752 LYS cc_start: 0.8087 (mmmt) cc_final: 0.7674 (mmmt) REVERT: A 768 GLU cc_start: 0.7606 (tt0) cc_final: 0.7278 (mt-10) REVERT: A 777 ASP cc_start: 0.7357 (p0) cc_final: 0.7136 (p0) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.0644 time to fit residues: 4.1966 Evaluate side-chains 45 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 3 optimal weight: 0.3980 chunk 5 optimal weight: 0.0980 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.184160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.157841 restraints weight = 4034.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.162892 restraints weight = 2669.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.166303 restraints weight = 1927.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.169095 restraints weight = 1500.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.171158 restraints weight = 1207.697| |-----------------------------------------------------------------------------| r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2147 Z= 0.132 Angle : 0.573 5.850 2922 Z= 0.292 Chirality : 0.048 0.136 320 Planarity : 0.004 0.038 391 Dihedral : 4.280 18.295 300 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.51), residues: 271 helix: -0.45 (0.63), residues: 60 sheet: 0.78 (0.65), residues: 60 loop : 0.11 (0.53), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 585 TYR 0.017 0.002 TYR A 765 PHE 0.020 0.003 PHE A 582 TRP 0.006 0.001 TRP A 646 HIS 0.002 0.001 HIS A 667 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 2147) covalent geometry : angle 0.57306 / 0.29 ( 2922) hydrogen bonds : bond 0.03383 / 2.33 ( 67) hydrogen bonds : angle 6.82899 / 4.60 ( 174) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 542 Ramachandran restraints generated. 271 Oldfield, 0 Emsley, 271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 542 Ramachandran restraints generated. 271 Oldfield, 0 Emsley, 271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.044 Fit side-chains revert: symmetry clash REVERT: A 540 ILE cc_start: 0.9221 (mt) cc_final: 0.8917 (mt) REVERT: A 558 ILE cc_start: 0.8684 (mt) cc_final: 0.8469 (mt) REVERT: A 583 LEU cc_start: 0.8223 (mt) cc_final: 0.7975 (mt) REVERT: A 585 ARG cc_start: 0.4941 (tpm170) cc_final: 0.1553 (mtp-110) REVERT: A 586 GLN cc_start: 0.8466 (mt0) cc_final: 0.8255 (mt0) REVERT: A 608 MET cc_start: 0.5885 (mpp) cc_final: 0.4265 (ptp) REVERT: A 734 ARG cc_start: 0.6296 (ttt180) cc_final: 0.6043 (tpt-90) REVERT: A 752 LYS cc_start: 0.7993 (mmmt) cc_final: 0.7677 (mmmt) REVERT: A 768 GLU cc_start: 0.7636 (tt0) cc_final: 0.7248 (mt-10) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0505 time to fit residues: 3.2049 Evaluate side-chains 45 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.0370 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 603 HIS A 792 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.181226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.155557 restraints weight = 3992.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.160183 restraints weight = 2655.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.163380 restraints weight = 1937.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.166026 restraints weight = 1520.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.167900 restraints weight = 1236.513| |-----------------------------------------------------------------------------| r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2147 Z= 0.161 Angle : 0.590 6.190 2922 Z= 0.301 Chirality : 0.049 0.141 320 Planarity : 0.004 0.040 391 Dihedral : 4.440 15.956 300 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.51), residues: 271 helix: -0.18 (0.67), residues: 57 sheet: 0.61 (0.64), residues: 60 loop : -0.07 (0.52), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 651 TYR 0.032 0.002 TYR A 765 PHE 0.021 0.003 PHE A 582 TRP 0.009 0.001 TRP A 646 HIS 0.003 0.001 HIS A 667 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 2147) covalent geometry : angle 0.58971 / 0.30 ( 2922) hydrogen bonds : bond 0.03268 / 2.21 ( 67) hydrogen bonds : angle 6.93977 / 4.71 ( 174) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 542 Ramachandran restraints generated. 271 Oldfield, 0 Emsley, 271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 542 Ramachandran restraints generated. 271 Oldfield, 0 Emsley, 271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.081 Fit side-chains revert: symmetry clash REVERT: A 540 ILE cc_start: 0.9294 (mt) cc_final: 0.8994 (mt) REVERT: A 585 ARG cc_start: 0.4903 (tpm170) cc_final: 0.2832 (tpm170) REVERT: A 752 LYS cc_start: 0.7903 (mmmt) cc_final: 0.7619 (mmmt) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.0726 time to fit residues: 4.7483 Evaluate side-chains 42 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 18 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4186 r_free = 0.4186 target = 0.180641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.154005 restraints weight = 4181.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.158616 restraints weight = 2902.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.162038 restraints weight = 2177.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.164443 restraints weight = 1723.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.166234 restraints weight = 1432.632| |-----------------------------------------------------------------------------| r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2147 Z= 0.174 Angle : 0.637 6.159 2922 Z= 0.326 Chirality : 0.050 0.141 320 Planarity : 0.005 0.039 391 Dihedral : 4.543 15.734 300 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.50), residues: 271 helix: -0.36 (0.66), residues: 58 sheet: 0.39 (0.62), residues: 65 loop : -0.27 (0.53), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 651 TYR 0.033 0.002 TYR A 765 PHE 0.026 0.002 PHE A 582 TRP 0.009 0.002 TRP A 646 HIS 0.006 0.001 HIS A 603 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 2147) covalent geometry : angle 0.63737 / 0.33 ( 2922) hydrogen bonds : bond 0.03468 / 2.31 ( 67) hydrogen bonds : angle 7.06341 / 4.75 ( 174) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 542 Ramachandran restraints generated. 271 Oldfield, 0 Emsley, 271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 542 Ramachandran restraints generated. 271 Oldfield, 0 Emsley, 271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 540 ILE cc_start: 0.9240 (mt) cc_final: 0.8902 (mt) REVERT: A 580 VAL cc_start: 0.8565 (t) cc_final: 0.7566 (t) REVERT: A 586 GLN cc_start: 0.8743 (mt0) cc_final: 0.8182 (mt0) REVERT: A 744 VAL cc_start: 0.8959 (p) cc_final: 0.8494 (m) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.0553 time to fit residues: 3.6844 Evaluate side-chains 49 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 7 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 6 optimal weight: 0.0670 chunk 16 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 726 HIS A 739 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.182226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.155026 restraints weight = 3962.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.159746 restraints weight = 2657.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.163320 restraints weight = 1970.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.165801 restraints weight = 1544.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.167854 restraints weight = 1276.897| |-----------------------------------------------------------------------------| r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2147 Z= 0.147 Angle : 0.633 10.115 2922 Z= 0.317 Chirality : 0.050 0.137 320 Planarity : 0.004 0.040 391 Dihedral : 4.601 18.775 300 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.51), residues: 271 helix: -0.11 (0.68), residues: 59 sheet: 0.38 (0.62), residues: 65 loop : -0.32 (0.53), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 651 TYR 0.030 0.002 TYR A 765 PHE 0.023 0.002 PHE A 582 TRP 0.008 0.001 TRP A 646 HIS 0.004 0.001 HIS A 598 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 2147) covalent geometry : angle 0.63347 / 0.32 ( 2922) hydrogen bonds : bond 0.03279 / 2.21 ( 67) hydrogen bonds : angle 6.87749 / 4.68 ( 174) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 542 Ramachandran restraints generated. 271 Oldfield, 0 Emsley, 271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 542 Ramachandran restraints generated. 271 Oldfield, 0 Emsley, 271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.070 Fit side-chains revert: symmetry clash REVERT: A 540 ILE cc_start: 0.9206 (mt) cc_final: 0.8883 (mt) REVERT: A 580 VAL cc_start: 0.8629 (t) cc_final: 0.7576 (t) REVERT: A 744 VAL cc_start: 0.8931 (p) cc_final: 0.8427 (m) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.0586 time to fit residues: 3.8961 Evaluate side-chains 52 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 26 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 5 optimal weight: 0.0970 chunk 8 optimal weight: 0.0980 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 739 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.183254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.156285 restraints weight = 4054.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.161048 restraints weight = 2725.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.164573 restraints weight = 2012.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.167126 restraints weight = 1581.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.168973 restraints weight = 1300.232| |-----------------------------------------------------------------------------| r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.5016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2147 Z= 0.139 Angle : 0.640 7.589 2922 Z= 0.326 Chirality : 0.050 0.137 320 Planarity : 0.004 0.041 391 Dihedral : 4.570 16.049 300 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.51), residues: 271 helix: -0.21 (0.66), residues: 60 sheet: 0.46 (0.63), residues: 65 loop : -0.47 (0.53), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 734 TYR 0.024 0.002 TYR A 765 PHE 0.016 0.002 PHE A 582 TRP 0.006 0.001 TRP A 646 HIS 0.003 0.001 HIS A 598 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 2147) covalent geometry : angle 0.63974 / 0.33 ( 2922) hydrogen bonds : bond 0.03081 / 2.00 ( 67) hydrogen bonds : angle 6.91558 / 4.64 ( 174) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 542 Ramachandran restraints generated. 271 Oldfield, 0 Emsley, 271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 542 Ramachandran restraints generated. 271 Oldfield, 0 Emsley, 271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.062 Fit side-chains revert: symmetry clash REVERT: A 580 VAL cc_start: 0.8509 (t) cc_final: 0.7360 (t) REVERT: A 585 ARG cc_start: 0.4591 (tpm170) cc_final: 0.1530 (mtp-110) REVERT: A 598 HIS cc_start: 0.7437 (t-170) cc_final: 0.7229 (t-170) REVERT: A 603 HIS cc_start: 0.4461 (m170) cc_final: 0.4146 (m170) REVERT: A 744 VAL cc_start: 0.8933 (p) cc_final: 0.8435 (m) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.0692 time to fit residues: 4.1551 Evaluate side-chains 46 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 14 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 20 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 5 optimal weight: 0.0670 chunk 23 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 739 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.183913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.156485 restraints weight = 4197.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.161316 restraints weight = 2819.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.164937 restraints weight = 2073.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.167420 restraints weight = 1629.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.169286 restraints weight = 1350.369| |-----------------------------------------------------------------------------| r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.5166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2147 Z= 0.142 Angle : 0.654 7.370 2922 Z= 0.331 Chirality : 0.050 0.151 320 Planarity : 0.004 0.041 391 Dihedral : 4.570 15.347 300 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.50), residues: 271 helix: -0.33 (0.66), residues: 60 sheet: 0.40 (0.64), residues: 65 loop : -0.53 (0.52), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 729 TYR 0.006 0.001 TYR A 632 PHE 0.016 0.002 PHE A 582 TRP 0.007 0.002 TRP A 646 HIS 0.002 0.001 HIS A 667 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 2147) covalent geometry : angle 0.65449 / 0.33 ( 2922) hydrogen bonds : bond 0.03388 / 2.23 ( 67) hydrogen bonds : angle 6.77871 / 4.55 ( 174) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 542 Ramachandran restraints generated. 271 Oldfield, 0 Emsley, 271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 542 Ramachandran restraints generated. 271 Oldfield, 0 Emsley, 271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.082 Fit side-chains REVERT: A 580 VAL cc_start: 0.8369 (t) cc_final: 0.7427 (t) REVERT: A 598 HIS cc_start: 0.7382 (t-170) cc_final: 0.7167 (t-170) REVERT: A 603 HIS cc_start: 0.4530 (m170) cc_final: 0.4175 (m170) REVERT: A 710 MET cc_start: 0.7714 (tpp) cc_final: 0.7032 (tpp) REVERT: A 744 VAL cc_start: 0.8919 (p) cc_final: 0.8407 (m) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0532 time to fit residues: 3.1388 Evaluate side-chains 44 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 0.0980 chunk 15 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 725 HIS A 739 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.181883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.154909 restraints weight = 4144.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.159519 restraints weight = 2737.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.162949 restraints weight = 2012.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.165346 restraints weight = 1584.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.167432 restraints weight = 1315.602| |-----------------------------------------------------------------------------| r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.5562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2147 Z= 0.163 Angle : 0.671 7.081 2922 Z= 0.341 Chirality : 0.050 0.140 320 Planarity : 0.005 0.039 391 Dihedral : 4.739 23.006 300 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.51), residues: 271 helix: -0.47 (0.66), residues: 60 sheet: 0.07 (0.72), residues: 55 loop : -0.46 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 729 TYR 0.010 0.002 TYR A 801 PHE 0.015 0.002 PHE A 582 TRP 0.011 0.002 TRP A 646 HIS 0.003 0.001 HIS A 667 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 ( 2147) covalent geometry : angle 0.67110 / 0.34 ( 2922) hydrogen bonds : bond 0.03434 / 2.24 ( 67) hydrogen bonds : angle 6.92513 / 4.64 ( 174) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 600.98 seconds wall clock time: 10 minutes 57.01 seconds (657.01 seconds total)