Starting phenix.real_space_refine on Wed Sep 17 04:20:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k6s_62134/09_2025/9k6s_62134.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k6s_62134/09_2025/9k6s_62134.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k6s_62134/09_2025/9k6s_62134.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k6s_62134/09_2025/9k6s_62134.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k6s_62134/09_2025/9k6s_62134.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k6s_62134/09_2025/9k6s_62134.map" } resolution = 2.8 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= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 38 5.49 5 Mg 1 5.21 5 S 19 5.16 5 C 2482 2.51 5 N 744 2.21 5 O 854 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4138 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3332 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 25, 'TRANS': 395} Chain breaks: 2 Chain: "B" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 401 Classifications: {'RNA': 19} Modifications used: {'p5*END': 1, 'rna2p_pyr': 3, 'rna3p_pur': 8, 'rna3p_pyr': 8} Link IDs: {'rna2p': 3, 'rna3p': 15} Chain: "C" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 404 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 9, 'rna3p_pyr': 6} Link IDs: {'rna2p': 3, 'rna3p': 15} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.34, per 1000 atoms: 0.32 Number of scatterers: 4138 At special positions: 0 Unit cell: (66.12, 77.52, 87.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 19 16.00 P 38 15.00 Mg 1 11.99 O 854 8.00 N 744 7.00 C 2482 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: 0.36 Conformation dependent library (CDL) restraints added in 149.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 788 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 2 sheets defined 35.4% alpha, 11.6% beta 13 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 463 through 481 Processing helix chain 'A' and resid 500 through 510 removed outlier: 3.954A pdb=" N MET A 504 " --> pdb=" O SER A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 538 removed outlier: 4.178A pdb=" N ALA A 530 " --> pdb=" O THR A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 554 removed outlier: 3.571A pdb=" N GLN A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG A 554 " --> pdb=" O LYS A 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 549 through 554' Processing helix chain 'A' and resid 556 through 572 removed outlier: 3.721A pdb=" N GLY A 572 " --> pdb=" O ASN A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 589 Processing helix chain 'A' and resid 641 through 658 removed outlier: 3.595A pdb=" N MET A 645 " --> pdb=" O ASP A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 680 removed outlier: 3.522A pdb=" N GLN A 675 " --> pdb=" O SER A 672 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE A 676 " --> pdb=" O GLU A 673 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N GLN A 677 " --> pdb=" O GLY A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 693 removed outlier: 3.695A pdb=" N LYS A 693 " --> pdb=" O GLU A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 789 Processing helix chain 'A' and resid 800 through 815 Processing helix chain 'A' and resid 840 through 846 Processing sheet with id=AA1, first strand: chain 'A' and resid 491 through 494 removed outlier: 4.191A pdb=" N LYS A 493 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ALA A 452 " --> pdb=" O VAL A 519 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ILE A 521 " --> pdb=" O ALA A 452 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ALA A 454 " --> pdb=" O ILE A 521 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 625 through 632 removed outlier: 5.600A pdb=" N PHE A 593 " --> pdb=" O SER A 617 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ILE A 664 " --> pdb=" O THR A 703 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N ILE A 705 " --> pdb=" O ILE A 664 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N PHE A 666 " --> pdb=" O ILE A 705 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL A 707 " --> pdb=" O PHE A 666 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ARG A 668 " --> pdb=" O VAL A 707 " (cutoff:3.500A) 121 hydrogen bonds defined for protein. 339 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 60 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 0.77 Time building geometry restraints manager: 0.50 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: 1078 1.34 - 1.45: 972 1.45 - 1.57: 2156 1.57 - 1.69: 74 1.69 - 1.81: 27 Bond restraints: 4307 Sorted by residual: bond pdb=" C GLU A 502 " pdb=" N PRO A 503 " ideal model delta sigma weight residual 1.336 1.375 -0.039 1.20e-02 6.94e+03 1.06e+01 bond pdb=" N VAL A 707 " pdb=" CA VAL A 707 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.14e-02 7.69e+03 9.09e+00 bond pdb=" N GLN A 633 " pdb=" CA GLN A 633 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.23e-02 6.61e+03 7.52e+00 bond pdb=" N ASP A 597 " pdb=" CA ASP A 597 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.21e-02 6.83e+03 7.26e+00 bond pdb=" N HIS A 634 " pdb=" CA HIS A 634 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.24e-02 6.50e+03 6.17e+00 ... (remaining 4302 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 5694 1.85 - 3.69: 262 3.69 - 5.54: 29 5.54 - 7.39: 25 7.39 - 9.24: 7 Bond angle restraints: 6017 Sorted by residual: angle pdb=" O2' U B 12 " pdb=" C2' U B 12 " pdb=" C1' U B 12 " ideal model delta sigma weight residual 111.80 102.56 9.24 1.50e+00 4.44e-01 3.79e+01 angle pdb=" N VAL A 552 " pdb=" CA VAL A 552 " pdb=" C VAL A 552 " ideal model delta sigma weight residual 112.96 108.09 4.87 1.00e+00 1.00e+00 2.38e+01 angle pdb=" N ARG A 814 " pdb=" CA ARG A 814 " pdb=" C ARG A 814 " ideal model delta sigma weight residual 111.36 106.96 4.40 1.09e+00 8.42e-01 1.63e+01 angle pdb=" C4' U B 12 " pdb=" O4' U B 12 " pdb=" C1' U B 12 " ideal model delta sigma weight residual 109.70 106.11 3.59 1.00e+00 1.00e+00 1.29e+01 angle pdb=" O3' G C 8 " pdb=" C3' G C 8 " pdb=" C2' G C 8 " ideal model delta sigma weight residual 113.70 119.06 -5.36 1.50e+00 4.44e-01 1.28e+01 ... (remaining 6012 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.92: 2371 30.92 - 61.83: 222 61.83 - 92.74: 39 92.74 - 123.66: 1 123.66 - 154.57: 2 Dihedral angle restraints: 2635 sinusoidal: 1413 harmonic: 1222 Sorted by residual: dihedral pdb=" O4' U C 20 " pdb=" C1' U C 20 " pdb=" N1 U C 20 " pdb=" C2 U C 20 " ideal model delta sinusoidal sigma weight residual 200.00 45.43 154.57 1 1.50e+01 4.44e-03 8.12e+01 dihedral pdb=" C5' U B 12 " pdb=" C4' U B 12 " pdb=" C3' U B 12 " pdb=" O3' U B 12 " ideal model delta sinusoidal sigma weight residual 147.00 94.76 52.24 1 8.00e+00 1.56e-02 5.82e+01 dihedral pdb=" O4' U B 12 " pdb=" C4' U B 12 " pdb=" C3' U B 12 " pdb=" C2' U B 12 " ideal model delta sinusoidal sigma weight residual 24.00 -23.29 47.29 1 8.00e+00 1.56e-02 4.83e+01 ... (remaining 2632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 656 0.109 - 0.219: 40 0.219 - 0.328: 3 0.328 - 0.438: 1 0.438 - 0.547: 7 Chirality restraints: 707 Sorted by residual: chirality pdb=" P U B 12 " pdb=" OP1 U B 12 " pdb=" OP2 U B 12 " pdb=" O5' U B 12 " both_signs ideal model delta sigma weight residual True 2.41 -2.96 -0.55 2.00e-01 2.50e+01 7.48e+00 chirality pdb=" P U B 13 " pdb=" OP1 U B 13 " pdb=" OP2 U B 13 " pdb=" O5' U B 13 " both_signs ideal model delta sigma weight residual True 2.41 -2.93 -0.52 2.00e-01 2.50e+01 6.76e+00 chirality pdb=" P U B 11 " pdb=" OP1 U B 11 " pdb=" OP2 U B 11 " pdb=" O5' U B 11 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.48e+00 ... (remaining 704 not shown) Planarity restraints: 635 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 814 " 0.867 9.50e-02 1.11e+02 3.89e-01 9.17e+01 pdb=" NE ARG A 814 " -0.052 2.00e-02 2.50e+03 pdb=" CZ ARG A 814 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 814 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 814 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 761 " -0.803 9.50e-02 1.11e+02 3.60e-01 7.89e+01 pdb=" NE ARG A 761 " 0.048 2.00e-02 2.50e+03 pdb=" CZ ARG A 761 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 761 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 761 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 710 " -0.205 9.50e-02 1.11e+02 9.17e-02 5.17e+00 pdb=" NE ARG A 710 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 710 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 710 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 710 " -0.007 2.00e-02 2.50e+03 ... (remaining 632 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 676 2.77 - 3.30: 3832 3.30 - 3.83: 7769 3.83 - 4.37: 8990 4.37 - 4.90: 13974 Nonbonded interactions: 35241 Sorted by model distance: nonbonded pdb=" OH TYR A 804 " pdb=" OP1 A B 5 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR A 765 " pdb=" O SER A 798 " model vdw 2.250 3.040 nonbonded pdb=" OG1 THR A 538 " pdb=" O GLN A 847 " model vdw 2.309 3.040 nonbonded pdb=" O GLN A 785 " pdb=" OG1 THR A 789 " model vdw 2.313 3.040 nonbonded pdb=" OG1 THR A 556 " pdb=" OG1 THR A 559 " model vdw 2.319 3.040 ... (remaining 35236 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: 0.260 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.180 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4755 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 : 0.005 0.039 4307 Z= 0.299 Angle : 0.944 9.236 6017 Z= 0.518 Chirality : 0.076 0.547 707 Planarity : 0.022 0.389 635 Dihedral : 22.124 154.571 1847 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.48 % Allowed : 5.30 % Favored : 94.22 % Rotamer: Outliers : 2.49 % Allowed : 30.19 % Favored : 67.31 % 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 aren not related in a simple way. whole: -1.58 (0.41), residues: 415 helix: -0.54 (0.41), residues: 145 sheet: -1.32 (0.58), residues: 81 loop : -1.20 (0.47), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 624 TYR 0.033 0.002 TYR A 815 PHE 0.011 0.002 PHE A 653 TRP 0.008 0.001 TRP A 435 HIS 0.008 0.001 HIS A 682 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 4307) covalent geometry : angle 0.94351 ( 6017) hydrogen bonds : bond 0.13169 ( 153) hydrogen bonds : angle 7.30653 ( 399) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 437 MET cc_start: 0.4543 (ttp) cc_final: 0.3784 (tpt) REVERT: A 545 GLN cc_start: 0.4820 (tp40) cc_final: 0.4530 (tp-100) REVERT: A 761 ARG cc_start: 0.3122 (OUTLIER) cc_final: 0.0422 (mmm160) outliers start: 9 outliers final: 1 residues processed: 69 average time/residue: 0.7120 time to fit residues: 50.5335 Evaluate side-chains 45 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 ARG Chi-restraints excluded: chain A residue 761 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.0980 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 0.0670 chunk 30 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 ASN A 562 ASN ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 HIS A 839 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5206 r_free = 0.5206 target = 0.295664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4896 r_free = 0.4896 target = 0.256393 restraints weight = 4617.865| |-----------------------------------------------------------------------------| r_work (start): 0.4921 rms_B_bonded: 2.18 r_work: 0.4821 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4783 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4307 Z= 0.129 Angle : 0.612 6.321 6017 Z= 0.317 Chirality : 0.043 0.200 707 Planarity : 0.005 0.045 635 Dihedral : 21.166 150.838 1047 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.99 % Allowed : 29.92 % Favored : 65.10 % 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 aren not related in a simple way. whole: -0.96 (0.42), residues: 415 helix: 0.34 (0.43), residues: 144 sheet: -1.20 (0.58), residues: 79 loop : -1.06 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 814 TYR 0.009 0.001 TYR A 765 PHE 0.021 0.002 PHE A 811 TRP 0.006 0.001 TRP A 435 HIS 0.007 0.001 HIS A 839 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 4307) covalent geometry : angle 0.61236 ( 6017) hydrogen bonds : bond 0.05167 ( 153) hydrogen bonds : angle 5.61287 ( 399) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.105 Fit side-chains REVERT: A 423 ARG cc_start: 0.6592 (ppt90) cc_final: 0.6369 (ppt90) REVERT: A 490 CYS cc_start: 0.2831 (OUTLIER) cc_final: 0.1813 (p) REVERT: A 505 PHE cc_start: 0.4762 (OUTLIER) cc_final: 0.3896 (t80) REVERT: A 663 ARG cc_start: 0.5247 (mpt-90) cc_final: 0.4940 (mmm-85) REVERT: A 666 PHE cc_start: 0.5066 (t80) cc_final: 0.4742 (t80) REVERT: A 814 ARG cc_start: 0.5799 (OUTLIER) cc_final: 0.5504 (mtt-85) outliers start: 18 outliers final: 2 residues processed: 63 average time/residue: 0.6469 time to fit residues: 42.1163 Evaluate side-chains 45 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 814 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 2 optimal weight: 0.0010 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 0.2980 chunk 6 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 ASN ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 772 ASN A 807 HIS A 839 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5215 r_free = 0.5215 target = 0.294270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4912 r_free = 0.4912 target = 0.256308 restraints weight = 4601.278| |-----------------------------------------------------------------------------| r_work (start): 0.4938 rms_B_bonded: 2.11 r_work: 0.4843 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4902 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4307 Z= 0.123 Angle : 0.601 5.648 6017 Z= 0.310 Chirality : 0.043 0.208 707 Planarity : 0.004 0.035 635 Dihedral : 20.904 149.797 1039 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 6.37 % Allowed : 29.64 % Favored : 63.99 % 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 aren not related in a simple way. whole: -0.80 (0.42), residues: 415 helix: 0.51 (0.44), residues: 147 sheet: -1.22 (0.56), residues: 79 loop : -0.97 (0.48), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 814 TYR 0.015 0.002 TYR A 667 PHE 0.025 0.002 PHE A 811 TRP 0.009 0.001 TRP A 769 HIS 0.006 0.001 HIS A 839 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 4307) covalent geometry : angle 0.60100 ( 6017) hydrogen bonds : bond 0.04757 ( 153) hydrogen bonds : angle 5.30459 ( 399) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 44 time to evaluate : 0.114 Fit side-chains REVERT: A 505 PHE cc_start: 0.5469 (OUTLIER) cc_final: 0.4916 (t80) REVERT: A 549 MET cc_start: 0.6662 (OUTLIER) cc_final: 0.6291 (ptt) REVERT: A 663 ARG cc_start: 0.5365 (mpt-90) cc_final: 0.5018 (mmm-85) REVERT: A 697 ASP cc_start: 0.5529 (OUTLIER) cc_final: 0.5134 (m-30) outliers start: 23 outliers final: 2 residues processed: 62 average time/residue: 0.4544 time to fit residues: 29.4088 Evaluate side-chains 42 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain A residue 736 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 36 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 28 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 ASN A 548 GLN ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 GLN ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 HIS A 839 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5118 r_free = 0.5118 target = 0.281207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.239964 restraints weight = 4485.680| |-----------------------------------------------------------------------------| r_work (start): 0.4807 rms_B_bonded: 2.12 r_work: 0.4700 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.4700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5181 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 4307 Z= 0.197 Angle : 0.710 9.081 6017 Z= 0.360 Chirality : 0.045 0.203 707 Planarity : 0.005 0.048 635 Dihedral : 20.862 148.112 1039 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.75 % Favored : 93.01 % Rotamer: Outliers : 6.37 % Allowed : 27.42 % Favored : 66.20 % 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 aren not related in a simple way. whole: -0.94 (0.42), residues: 415 helix: 0.19 (0.42), residues: 148 sheet: -1.17 (0.54), residues: 84 loop : -0.90 (0.49), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 814 TYR 0.020 0.002 TYR A 667 PHE 0.030 0.002 PHE A 811 TRP 0.006 0.001 TRP A 451 HIS 0.005 0.001 HIS A 788 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 4307) covalent geometry : angle 0.71009 ( 6017) hydrogen bonds : bond 0.06004 ( 153) hydrogen bonds : angle 5.45565 ( 399) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 45 time to evaluate : 0.133 Fit side-chains revert: symmetry clash REVERT: A 505 PHE cc_start: 0.5336 (OUTLIER) cc_final: 0.4564 (t80) REVERT: A 542 MET cc_start: 0.5497 (pmm) cc_final: 0.4598 (ptp) REVERT: A 549 MET cc_start: 0.6546 (OUTLIER) cc_final: 0.5983 (ptm) REVERT: A 639 ILE cc_start: 0.4539 (OUTLIER) cc_final: 0.3930 (mm) outliers start: 23 outliers final: 5 residues processed: 63 average time/residue: 0.5431 time to fit residues: 35.5212 Evaluate side-chains 49 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 811 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 21 optimal weight: 0.5980 chunk 19 optimal weight: 0.0770 chunk 43 optimal weight: 20.0000 chunk 10 optimal weight: 0.2980 chunk 8 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 ASN A 548 GLN ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5159 r_free = 0.5159 target = 0.285089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.246618 restraints weight = 4456.578| |-----------------------------------------------------------------------------| r_work (start): 0.4866 rms_B_bonded: 1.94 r_work: 0.4730 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5192 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4307 Z= 0.126 Angle : 0.608 6.791 6017 Z= 0.311 Chirality : 0.043 0.202 707 Planarity : 0.004 0.036 635 Dihedral : 20.713 149.569 1039 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 4.71 % Allowed : 29.09 % Favored : 66.20 % 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 aren not related in a simple way. whole: -0.64 (0.42), residues: 415 helix: 0.66 (0.44), residues: 148 sheet: -1.32 (0.52), residues: 80 loop : -0.78 (0.49), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 814 TYR 0.018 0.002 TYR A 667 PHE 0.014 0.001 PHE A 811 TRP 0.004 0.001 TRP A 769 HIS 0.012 0.001 HIS A 807 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 4307) covalent geometry : angle 0.60792 ( 6017) hydrogen bonds : bond 0.04573 ( 153) hydrogen bonds : angle 5.15392 ( 399) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: A 505 PHE cc_start: 0.5740 (OUTLIER) cc_final: 0.4995 (t80) REVERT: A 542 MET cc_start: 0.5231 (pmm) cc_final: 0.4430 (ptp) REVERT: A 548 GLN cc_start: 0.5355 (OUTLIER) cc_final: 0.5106 (tt0) REVERT: A 549 MET cc_start: 0.6470 (OUTLIER) cc_final: 0.6095 (ptm) REVERT: A 626 CYS cc_start: 0.5242 (t) cc_final: 0.5004 (m) REVERT: A 774 PHE cc_start: 0.5923 (OUTLIER) cc_final: 0.5560 (m-10) outliers start: 17 outliers final: 5 residues processed: 58 average time/residue: 0.3922 time to fit residues: 23.9455 Evaluate side-chains 49 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 774 PHE Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 839 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 38 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 ASN A 548 GLN ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 ASN A 839 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5098 r_free = 0.5098 target = 0.276068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.235081 restraints weight = 4565.460| |-----------------------------------------------------------------------------| r_work (start): 0.4764 rms_B_bonded: 1.99 r_work: 0.4620 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5430 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 4307 Z= 0.215 Angle : 0.706 7.417 6017 Z= 0.361 Chirality : 0.046 0.202 707 Planarity : 0.005 0.046 635 Dihedral : 20.800 148.456 1039 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.47 % Favored : 92.29 % Rotamer: Outliers : 8.03 % Allowed : 27.15 % Favored : 64.82 % 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 aren not related in a simple way. whole: -0.66 (0.43), residues: 415 helix: 0.51 (0.43), residues: 148 sheet: -1.31 (0.50), residues: 94 loop : -0.59 (0.52), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 814 TYR 0.021 0.003 TYR A 667 PHE 0.022 0.002 PHE A 811 TRP 0.003 0.001 TRP A 769 HIS 0.037 0.003 HIS A 839 Details of bonding type rmsd covalent geometry : bond 0.00503 ( 4307) covalent geometry : angle 0.70562 ( 6017) hydrogen bonds : bond 0.06096 ( 153) hydrogen bonds : angle 5.31471 ( 399) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 41 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 479 ARG cc_start: 0.7301 (tpp-160) cc_final: 0.6770 (mmm-85) REVERT: A 505 PHE cc_start: 0.5841 (OUTLIER) cc_final: 0.4931 (t80) REVERT: A 542 MET cc_start: 0.5378 (pmm) cc_final: 0.4872 (ptp) REVERT: A 639 ILE cc_start: 0.4393 (OUTLIER) cc_final: 0.3908 (mm) REVERT: A 702 ILE cc_start: 0.5009 (OUTLIER) cc_final: 0.4393 (mt) REVERT: A 774 PHE cc_start: 0.6157 (OUTLIER) cc_final: 0.5757 (m-10) outliers start: 29 outliers final: 10 residues processed: 64 average time/residue: 0.4517 time to fit residues: 30.0372 Evaluate side-chains 51 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 37 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 647 ARG Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 774 PHE Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain A residue 811 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 18 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 43 optimal weight: 20.0000 chunk 32 optimal weight: 8.9990 chunk 1 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 ASN A 548 GLN ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 ASN A 708 GLN A 764 HIS A 839 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5113 r_free = 0.5113 target = 0.278228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.238544 restraints weight = 4541.727| |-----------------------------------------------------------------------------| r_work (start): 0.4791 rms_B_bonded: 1.93 r_work: 0.4652 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5345 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 4307 Z= 0.167 Angle : 0.690 14.060 6017 Z= 0.348 Chirality : 0.044 0.201 707 Planarity : 0.005 0.044 635 Dihedral : 20.748 148.982 1039 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 20.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 7.48 % Allowed : 27.15 % Favored : 65.37 % 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 aren not related in a simple way. whole: -0.74 (0.42), residues: 415 helix: 0.61 (0.44), residues: 148 sheet: -1.57 (0.47), residues: 92 loop : -0.68 (0.52), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 423 TYR 0.013 0.002 TYR A 749 PHE 0.016 0.002 PHE A 811 TRP 0.003 0.001 TRP A 435 HIS 0.010 0.002 HIS A 807 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 4307) covalent geometry : angle 0.69021 ( 6017) hydrogen bonds : bond 0.05317 ( 153) hydrogen bonds : angle 5.35360 ( 399) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 40 time to evaluate : 0.086 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 479 ARG cc_start: 0.7291 (tpp-160) cc_final: 0.6687 (mmm-85) REVERT: A 505 PHE cc_start: 0.5823 (OUTLIER) cc_final: 0.4928 (t80) REVERT: A 542 MET cc_start: 0.5552 (pmm) cc_final: 0.5114 (ptp) REVERT: A 548 GLN cc_start: 0.5481 (OUTLIER) cc_final: 0.5191 (mt0) REVERT: A 630 ARG cc_start: 0.5209 (OUTLIER) cc_final: 0.4987 (tpp80) REVERT: A 639 ILE cc_start: 0.4367 (OUTLIER) cc_final: 0.3843 (mm) REVERT: A 702 ILE cc_start: 0.4151 (OUTLIER) cc_final: 0.3560 (mp) REVERT: A 839 HIS cc_start: 0.6613 (OUTLIER) cc_final: 0.6018 (p-80) outliers start: 27 outliers final: 9 residues processed: 62 average time/residue: 0.5751 time to fit residues: 36.9458 Evaluate side-chains 50 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 35 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 630 ARG Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 647 ARG Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 839 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 10 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 43 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 GLN ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 ASN A 600 HIS A 708 GLN A 764 HIS A 839 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5109 r_free = 0.5109 target = 0.277903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.238539 restraints weight = 4481.310| |-----------------------------------------------------------------------------| r_work (start): 0.4791 rms_B_bonded: 1.91 r_work: 0.4648 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5387 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4307 Z= 0.173 Angle : 0.688 11.554 6017 Z= 0.348 Chirality : 0.045 0.215 707 Planarity : 0.005 0.045 635 Dihedral : 20.742 149.364 1039 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 5.82 % Allowed : 29.64 % Favored : 64.54 % 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 aren not related in a simple way. whole: -0.76 (0.42), residues: 415 helix: 0.57 (0.44), residues: 148 sheet: -1.59 (0.47), residues: 92 loop : -0.66 (0.52), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 423 TYR 0.016 0.002 TYR A 667 PHE 0.016 0.002 PHE A 811 TRP 0.003 0.001 TRP A 435 HIS 0.009 0.002 HIS A 807 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 4307) covalent geometry : angle 0.68790 ( 6017) hydrogen bonds : bond 0.05336 ( 153) hydrogen bonds : angle 5.37024 ( 399) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 40 time to evaluate : 0.083 Fit side-chains revert: symmetry clash REVERT: A 505 PHE cc_start: 0.5946 (OUTLIER) cc_final: 0.5052 (t80) REVERT: A 542 MET cc_start: 0.5630 (pmm) cc_final: 0.5093 (ptp) REVERT: A 549 MET cc_start: 0.6500 (OUTLIER) cc_final: 0.6172 (ptm) REVERT: A 630 ARG cc_start: 0.5113 (OUTLIER) cc_final: 0.4902 (tpp80) REVERT: A 639 ILE cc_start: 0.4264 (OUTLIER) cc_final: 0.3761 (mm) REVERT: A 702 ILE cc_start: 0.4090 (OUTLIER) cc_final: 0.3390 (mp) outliers start: 21 outliers final: 8 residues processed: 56 average time/residue: 0.5363 time to fit residues: 31.1201 Evaluate side-chains 49 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 630 ARG Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 647 ARG Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 709 LYS Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 738 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 38 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 31 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 GLN A 548 GLN ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 ASN A 708 GLN A 764 HIS A 807 HIS A 839 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5101 r_free = 0.5101 target = 0.280531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.239028 restraints weight = 4508.497| |-----------------------------------------------------------------------------| r_work (start): 0.4781 rms_B_bonded: 2.08 r_work: 0.4677 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.4677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5208 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4307 Z= 0.168 Angle : 0.675 10.123 6017 Z= 0.342 Chirality : 0.045 0.201 707 Planarity : 0.005 0.045 635 Dihedral : 20.730 149.788 1039 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 20.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 5.82 % Allowed : 29.64 % Favored : 64.54 % 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 aren not related in a simple way. whole: -0.80 (0.43), residues: 415 helix: 0.57 (0.44), residues: 148 sheet: -1.60 (0.48), residues: 92 loop : -0.72 (0.52), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 423 TYR 0.019 0.003 TYR A 784 PHE 0.009 0.002 PHE A 811 TRP 0.003 0.001 TRP A 435 HIS 0.011 0.002 HIS A 807 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 4307) covalent geometry : angle 0.67470 ( 6017) hydrogen bonds : bond 0.05260 ( 153) hydrogen bonds : angle 5.32365 ( 399) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 41 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: A 505 PHE cc_start: 0.5559 (OUTLIER) cc_final: 0.4669 (t80) REVERT: A 542 MET cc_start: 0.5765 (pmm) cc_final: 0.5133 (ptp) REVERT: A 548 GLN cc_start: 0.5791 (OUTLIER) cc_final: 0.5425 (tt0) REVERT: A 630 ARG cc_start: 0.5110 (OUTLIER) cc_final: 0.4862 (tpp80) REVERT: A 639 ILE cc_start: 0.4135 (OUTLIER) cc_final: 0.3678 (mm) REVERT: A 702 ILE cc_start: 0.3958 (OUTLIER) cc_final: 0.3294 (mp) outliers start: 21 outliers final: 10 residues processed: 58 average time/residue: 0.5326 time to fit residues: 32.1204 Evaluate side-chains 53 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 630 ARG Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 647 ARG Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 709 LYS Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 807 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 2 optimal weight: 0.0970 chunk 33 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 GLN A 548 GLN ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 ASN A 708 GLN A 839 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5122 r_free = 0.5122 target = 0.280124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.241741 restraints weight = 4484.037| |-----------------------------------------------------------------------------| r_work (start): 0.4806 rms_B_bonded: 1.88 r_work: 0.4667 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5317 moved from start: 0.4783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4307 Z= 0.150 Angle : 0.665 9.301 6017 Z= 0.336 Chirality : 0.045 0.201 707 Planarity : 0.005 0.043 635 Dihedral : 20.689 150.349 1039 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 19.45 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.02 % Favored : 93.73 % Rotamer: Outliers : 4.99 % Allowed : 30.19 % Favored : 64.82 % 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 aren not related in a simple way. whole: -0.77 (0.42), residues: 415 helix: 0.71 (0.44), residues: 147 sheet: -1.47 (0.51), residues: 81 loop : -0.96 (0.49), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 423 TYR 0.018 0.002 TYR A 667 PHE 0.010 0.002 PHE A 587 TRP 0.022 0.003 TRP A 451 HIS 0.020 0.002 HIS A 807 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 4307) covalent geometry : angle 0.66466 ( 6017) hydrogen bonds : bond 0.04991 ( 153) hydrogen bonds : angle 5.29281 ( 399) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 39 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: A 437 MET cc_start: 0.4859 (ttp) cc_final: 0.4522 (tpt) REVERT: A 505 PHE cc_start: 0.5838 (OUTLIER) cc_final: 0.4967 (t80) REVERT: A 542 MET cc_start: 0.5451 (pmm) cc_final: 0.4936 (ptp) REVERT: A 548 GLN cc_start: 0.5497 (OUTLIER) cc_final: 0.5110 (tt0) REVERT: A 626 CYS cc_start: 0.5640 (t) cc_final: 0.5116 (m) REVERT: A 639 ILE cc_start: 0.4224 (OUTLIER) cc_final: 0.3846 (mm) REVERT: A 668 ARG cc_start: 0.6815 (tpt170) cc_final: 0.6516 (tpt170) REVERT: A 702 ILE cc_start: 0.3876 (OUTLIER) cc_final: 0.3121 (mp) outliers start: 18 outliers final: 8 residues processed: 54 average time/residue: 0.5556 time to fit residues: 31.0579 Evaluate side-chains 48 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 647 ARG Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 738 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 27 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 3 optimal weight: 0.0970 chunk 2 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 GLN A 548 GLN ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 ASN A 708 GLN A 807 HIS A 839 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5116 r_free = 0.5116 target = 0.283840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.243154 restraints weight = 4533.960| |-----------------------------------------------------------------------------| r_work (start): 0.4823 rms_B_bonded: 2.13 r_work: 0.4722 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5143 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4307 Z= 0.145 Angle : 0.654 8.853 6017 Z= 0.332 Chirality : 0.044 0.201 707 Planarity : 0.005 0.043 635 Dihedral : 20.657 150.779 1039 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 4.99 % Allowed : 30.19 % Favored : 64.82 % 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 aren not related in a simple way. whole: -0.79 (0.42), residues: 415 helix: 0.68 (0.44), residues: 147 sheet: -1.50 (0.51), residues: 81 loop : -0.95 (0.49), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 423 TYR 0.029 0.003 TYR A 784 PHE 0.008 0.002 PHE A 587 TRP 0.039 0.004 TRP A 451 HIS 0.012 0.002 HIS A 807 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 4307) covalent geometry : angle 0.65378 ( 6017) hydrogen bonds : bond 0.04948 ( 153) hydrogen bonds : angle 5.24497 ( 399) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1556.62 seconds wall clock time: 27 minutes 22.98 seconds (1642.98 seconds total)