Starting phenix.real_space_refine on Wed Jul 23 18:30:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k6s_62134/07_2025/9k6s_62134.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k6s_62134/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9k6s_62134/07_2025/9k6s_62134.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k6s_62134/07_2025/9k6s_62134.map" model { file = "/net/cci-nas-00/data/ceres_data/9k6s_62134/07_2025/9k6s_62134.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k6s_62134/07_2025/9k6s_62134.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 4.23, per 1000 atoms: 1.02 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: 2.19 Conformation dependent library (CDL) restraints added in 729.4 milliseconds 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: 3.42 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: 2.70 Time building geometry restraints manager: 2.32 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: 9.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 27.000 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:43.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.680 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP A 435 HIS 0.008 0.001 HIS A 682 PHE 0.011 0.002 PHE A 653 TYR 0.033 0.002 TYR A 815 ARG 0.014 0.001 ARG A 624 Details of bonding type rmsd hydrogen bonds : bond 0.13169 ( 153) hydrogen bonds : angle 7.30653 ( 399) covalent geometry : bond 0.00511 ( 4307) covalent geometry : angle 0.94351 ( 6017) *********************** 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 : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 437 MET cc_start: 0.4543 (ttp) cc_final: 0.3785 (tpt) REVERT: A 545 GLN cc_start: 0.4820 (tp40) cc_final: 0.4529 (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: 1.4244 time to fit residues: 101.3631 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 : 0.476 ------------------------------------------------------------------------------- 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 37 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.5194 r_free = 0.5194 target = 0.290943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4874 r_free = 0.4874 target = 0.251568 restraints weight = 4503.425| |-----------------------------------------------------------------------------| r_work (start): 0.4903 rms_B_bonded: 2.11 r_work: 0.4800 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4950 moved from start: 0.2069 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= 0.153 Angle : 0.640 6.265 6017 Z= 0.330 Chirality : 0.043 0.200 707 Planarity : 0.005 0.045 635 Dihedral : 21.174 150.425 1047 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 5.54 % Allowed : 30.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.42), residues: 415 helix: 0.34 (0.43), residues: 145 sheet: -1.07 (0.58), residues: 79 loop : -1.05 (0.47), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 435 HIS 0.006 0.001 HIS A 839 PHE 0.021 0.002 PHE A 811 TYR 0.009 0.002 TYR A 815 ARG 0.005 0.000 ARG A 814 Details of bonding type rmsd hydrogen bonds : bond 0.05402 ( 153) hydrogen bonds : angle 5.59820 ( 399) covalent geometry : bond 0.00344 ( 4307) covalent geometry : angle 0.64042 ( 6017) *********************** 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 69 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 49 time to evaluate : 0.377 Fit side-chains REVERT: A 505 PHE cc_start: 0.5196 (OUTLIER) cc_final: 0.4566 (t80) REVERT: A 542 MET cc_start: 0.5282 (pmm) cc_final: 0.4898 (pmm) REVERT: A 663 ARG cc_start: 0.5271 (mpt-90) cc_final: 0.4971 (mmm-85) REVERT: A 710 ARG cc_start: 0.4743 (OUTLIER) cc_final: 0.3105 (tmt-80) REVERT: A 807 HIS cc_start: 0.6248 (t-90) cc_final: 0.6005 (t-170) REVERT: A 814 ARG cc_start: 0.5840 (OUTLIER) cc_final: 0.5547 (mtt-85) outliers start: 20 outliers final: 3 residues processed: 61 average time/residue: 1.1585 time to fit residues: 73.3119 Evaluate side-chains 51 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 710 ARG 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 4 optimal weight: 0.0870 chunk 19 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 14 optimal weight: 0.0570 chunk 5 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 43 optimal weight: 20.0000 chunk 10 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 17 optimal weight: 0.1980 overall best weight: 0.4076 ------------------------------------------------------------------------------- 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 = 0.5200 r_free = 0.5200 target = 0.292689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4899 r_free = 0.4899 target = 0.254703 restraints weight = 4511.622| |-----------------------------------------------------------------------------| r_work (start): 0.4925 rms_B_bonded: 2.09 r_work: 0.4825 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4916 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4307 Z= 0.118 Angle : 0.585 5.852 6017 Z= 0.302 Chirality : 0.043 0.229 707 Planarity : 0.004 0.035 635 Dihedral : 20.979 150.062 1043 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 7.20 % Allowed : 27.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.42), residues: 415 helix: 0.54 (0.44), residues: 147 sheet: -1.09 (0.57), residues: 79 loop : -1.01 (0.47), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 769 HIS 0.006 0.001 HIS A 839 PHE 0.009 0.001 PHE A 858 TYR 0.015 0.002 TYR A 667 ARG 0.004 0.000 ARG A 814 Details of bonding type rmsd hydrogen bonds : bond 0.04594 ( 153) hydrogen bonds : angle 5.30281 ( 399) covalent geometry : bond 0.00263 ( 4307) covalent geometry : angle 0.58491 ( 6017) *********************** 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 71 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 45 time to evaluate : 0.389 Fit side-chains REVERT: A 423 ARG cc_start: 0.6594 (ppt90) cc_final: 0.6251 (ppt90) REVERT: A 505 PHE cc_start: 0.5331 (OUTLIER) cc_final: 0.4898 (m-80) REVERT: A 542 MET cc_start: 0.5154 (pmm) cc_final: 0.4892 (pmm) REVERT: A 549 MET cc_start: 0.6620 (OUTLIER) cc_final: 0.6184 (ptm) REVERT: A 663 ARG cc_start: 0.5337 (mpt-90) cc_final: 0.4992 (mmm-85) REVERT: A 697 ASP cc_start: 0.5627 (OUTLIER) cc_final: 0.5208 (m-30) REVERT: A 710 ARG cc_start: 0.4771 (OUTLIER) cc_final: 0.3056 (tmt-80) outliers start: 26 outliers final: 3 residues processed: 65 average time/residue: 1.0140 time to fit residues: 68.7093 Evaluate side-chains 44 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 710 ARG Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 738 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 40 optimal weight: 3.9990 chunk 43 optimal weight: 20.0000 chunk 41 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 772 ASN 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 = 0.5104 r_free = 0.5104 target = 0.279584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.238556 restraints weight = 4460.632| |-----------------------------------------------------------------------------| r_work (start): 0.4785 rms_B_bonded: 2.11 r_work: 0.4681 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5207 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 4307 Z= 0.196 Angle : 0.713 8.542 6017 Z= 0.358 Chirality : 0.045 0.202 707 Planarity : 0.005 0.053 635 Dihedral : 20.906 148.011 1043 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.23 % Favored : 92.53 % Rotamer: Outliers : 6.93 % Allowed : 27.42 % Favored : 65.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.42), residues: 415 helix: 0.22 (0.42), residues: 148 sheet: -1.03 (0.55), residues: 84 loop : -0.90 (0.49), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 769 HIS 0.005 0.001 HIS A 788 PHE 0.015 0.002 PHE A 858 TYR 0.017 0.002 TYR A 667 ARG 0.004 0.000 ARG A 814 Details of bonding type rmsd hydrogen bonds : bond 0.06075 ( 153) hydrogen bonds : angle 5.44632 ( 399) covalent geometry : bond 0.00458 ( 4307) covalent geometry : angle 0.71268 ( 6017) *********************** 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 69 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 44 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 505 PHE cc_start: 0.5447 (OUTLIER) cc_final: 0.4724 (t80) REVERT: A 516 GLN cc_start: 0.7176 (OUTLIER) cc_final: 0.6913 (pt0) REVERT: A 542 MET cc_start: 0.5438 (pmm) cc_final: 0.4753 (ptp) REVERT: A 549 MET cc_start: 0.6596 (OUTLIER) cc_final: 0.6044 (ptm) REVERT: A 666 PHE cc_start: 0.5629 (t80) cc_final: 0.5361 (t80) REVERT: A 668 ARG cc_start: 0.6729 (tpt170) cc_final: 0.6513 (tpt90) REVERT: A 710 ARG cc_start: 0.4709 (OUTLIER) cc_final: 0.2877 (tmt-80) REVERT: A 774 PHE cc_start: 0.5892 (OUTLIER) cc_final: 0.5562 (m-10) outliers start: 25 outliers final: 5 residues processed: 63 average time/residue: 1.0903 time to fit residues: 71.4238 Evaluate side-chains 52 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 516 GLN 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 647 ARG Chi-restraints excluded: chain A residue 710 ARG Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 774 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 17 optimal weight: 0.0170 chunk 42 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 15 optimal weight: 0.0980 chunk 14 optimal weight: 3.9990 overall best weight: 1.0222 ------------------------------------------------------------------------------- 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 708 GLN ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5118 r_free = 0.5118 target = 0.279749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.239666 restraints weight = 4515.364| |-----------------------------------------------------------------------------| r_work (start): 0.4787 rms_B_bonded: 1.98 r_work: 0.4654 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5310 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4307 Z= 0.160 Angle : 0.639 6.268 6017 Z= 0.325 Chirality : 0.043 0.200 707 Planarity : 0.005 0.042 635 Dihedral : 20.822 148.627 1043 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 5.82 % Allowed : 27.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.42), residues: 415 helix: 0.72 (0.44), residues: 142 sheet: -1.04 (0.54), residues: 84 loop : -0.80 (0.48), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 451 HIS 0.005 0.001 HIS A 443 PHE 0.009 0.001 PHE A 858 TYR 0.017 0.002 TYR A 804 ARG 0.007 0.001 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.05222 ( 153) hydrogen bonds : angle 5.29985 ( 399) covalent geometry : bond 0.00367 ( 4307) covalent geometry : angle 0.63912 ( 6017) *********************** 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: 21 poor density : 41 time to evaluate : 0.437 Fit side-chains REVERT: A 505 PHE cc_start: 0.5743 (OUTLIER) cc_final: 0.4970 (t80) REVERT: A 516 GLN cc_start: 0.7220 (OUTLIER) cc_final: 0.6958 (pt0) REVERT: A 542 MET cc_start: 0.5496 (pmm) cc_final: 0.5001 (ptp) REVERT: A 549 MET cc_start: 0.6510 (OUTLIER) cc_final: 0.6093 (ptm) REVERT: A 576 ASN cc_start: 0.6839 (p0) cc_final: 0.6496 (p0) REVERT: A 639 ILE cc_start: 0.4411 (OUTLIER) cc_final: 0.3865 (mm) REVERT: A 702 ILE cc_start: 0.5114 (OUTLIER) cc_final: 0.4509 (mp) REVERT: A 710 ARG cc_start: 0.4801 (OUTLIER) cc_final: 0.2993 (tpt90) outliers start: 21 outliers final: 3 residues processed: 56 average time/residue: 1.1345 time to fit residues: 66.1508 Evaluate side-chains 46 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 516 GLN Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 710 ARG Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 738 THR 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 30 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 43 optimal weight: 20.0000 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 708 GLN A 839 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5083 r_free = 0.5083 target = 0.278717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.236625 restraints weight = 4502.418| |-----------------------------------------------------------------------------| r_work (start): 0.4750 rms_B_bonded: 2.17 r_work: 0.4649 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5227 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 4307 Z= 0.199 Angle : 0.673 6.954 6017 Z= 0.343 Chirality : 0.045 0.200 707 Planarity : 0.005 0.047 635 Dihedral : 20.860 148.369 1043 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.47 % Favored : 92.29 % Rotamer: Outliers : 5.26 % Allowed : 29.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.42), residues: 415 helix: 0.62 (0.44), residues: 142 sheet: -1.25 (0.50), residues: 95 loop : -0.67 (0.51), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 435 HIS 0.019 0.002 HIS A 839 PHE 0.013 0.002 PHE A 587 TYR 0.016 0.002 TYR A 667 ARG 0.004 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.05785 ( 153) hydrogen bonds : angle 5.39893 ( 399) covalent geometry : bond 0.00462 ( 4307) covalent geometry : angle 0.67298 ( 6017) *********************** 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 58 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 39 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 505 PHE cc_start: 0.5485 (OUTLIER) cc_final: 0.4662 (t80) REVERT: A 516 GLN cc_start: 0.7333 (OUTLIER) cc_final: 0.7040 (pt0) REVERT: A 542 MET cc_start: 0.6018 (pmm) cc_final: 0.5361 (ptp) REVERT: A 639 ILE cc_start: 0.4303 (OUTLIER) cc_final: 0.3767 (mm) REVERT: A 668 ARG cc_start: 0.6820 (tpt170) cc_final: 0.6578 (tpt90) REVERT: A 702 ILE cc_start: 0.5005 (OUTLIER) cc_final: 0.4503 (mt) REVERT: A 710 ARG cc_start: 0.4335 (tmt90) cc_final: 0.2574 (tpt90) outliers start: 19 outliers final: 7 residues processed: 57 average time/residue: 1.1643 time to fit residues: 68.9933 Evaluate side-chains 44 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 516 GLN Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 555 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 27 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 30 optimal weight: 0.1980 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 600 HIS A 764 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 = 0.5116 r_free = 0.5116 target = 0.282133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.242954 restraints weight = 4503.262| |-----------------------------------------------------------------------------| r_work (start): 0.4804 rms_B_bonded: 2.13 r_work: 0.4707 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5164 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4307 Z= 0.142 Angle : 0.621 6.739 6017 Z= 0.316 Chirality : 0.043 0.199 707 Planarity : 0.004 0.042 635 Dihedral : 20.761 149.835 1039 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 4.71 % Allowed : 30.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.42), residues: 415 helix: 0.71 (0.45), residues: 148 sheet: -1.35 (0.49), residues: 92 loop : -0.77 (0.51), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 769 HIS 0.006 0.001 HIS A 788 PHE 0.014 0.002 PHE A 587 TYR 0.013 0.002 TYR A 667 ARG 0.003 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04885 ( 153) hydrogen bonds : angle 5.26687 ( 399) covalent geometry : bond 0.00325 ( 4307) covalent geometry : angle 0.62111 ( 6017) *********************** 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 63 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.411 Fit side-chains REVERT: A 479 ARG cc_start: 0.6945 (tpp-160) cc_final: 0.6384 (mmm-85) REVERT: A 505 PHE cc_start: 0.5644 (OUTLIER) cc_final: 0.4867 (t80) REVERT: A 516 GLN cc_start: 0.7328 (OUTLIER) cc_final: 0.7046 (pt0) REVERT: A 542 MET cc_start: 0.5945 (pmm) cc_final: 0.5274 (ptp) REVERT: A 548 GLN cc_start: 0.5572 (OUTLIER) cc_final: 0.5265 (tt0) REVERT: A 639 ILE cc_start: 0.4125 (OUTLIER) cc_final: 0.3648 (mm) REVERT: A 710 ARG cc_start: 0.4268 (tmt90) cc_final: 0.2528 (tmt-80) outliers start: 17 outliers final: 6 residues processed: 61 average time/residue: 1.0270 time to fit residues: 65.3956 Evaluate side-chains 48 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 516 GLN Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 586 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 839 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 32 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 GLN ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 HIS A 839 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5124 r_free = 0.5124 target = 0.280785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.241903 restraints weight = 4431.278| |-----------------------------------------------------------------------------| r_work (start): 0.4808 rms_B_bonded: 1.96 r_work: 0.4666 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5340 moved from start: 0.4458 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 : 0.640 6.498 6017 Z= 0.324 Chirality : 0.043 0.200 707 Planarity : 0.005 0.043 635 Dihedral : 20.743 150.379 1039 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 3.88 % Allowed : 31.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.42), residues: 415 helix: 0.88 (0.45), residues: 141 sheet: -1.17 (0.52), residues: 82 loop : -1.00 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 435 HIS 0.006 0.001 HIS A 764 PHE 0.011 0.002 PHE A 587 TYR 0.019 0.002 TYR A 784 ARG 0.003 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.05015 ( 153) hydrogen bonds : angle 5.29873 ( 399) covalent geometry : bond 0.00346 ( 4307) covalent geometry : angle 0.64026 ( 6017) *********************** 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 54 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.377 Fit side-chains REVERT: A 479 ARG cc_start: 0.7076 (tpp-160) cc_final: 0.6595 (mmm-85) REVERT: A 505 PHE cc_start: 0.5862 (OUTLIER) cc_final: 0.5053 (t80) REVERT: A 516 GLN cc_start: 0.7235 (OUTLIER) cc_final: 0.6914 (pt0) REVERT: A 542 MET cc_start: 0.5714 (pmm) cc_final: 0.5270 (ptp) REVERT: A 548 GLN cc_start: 0.5518 (OUTLIER) cc_final: 0.5142 (tt0) REVERT: A 576 ASN cc_start: 0.7025 (p0) cc_final: 0.6667 (p0) REVERT: A 710 ARG cc_start: 0.4514 (tmt90) cc_final: 0.2821 (tmt-80) REVERT: A 839 HIS cc_start: 0.6392 (OUTLIER) cc_final: 0.5856 (p90) outliers start: 14 outliers final: 5 residues processed: 52 average time/residue: 0.9860 time to fit residues: 53.5932 Evaluate side-chains 46 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 516 GLN 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 586 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 839 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 11 optimal weight: 0.0870 chunk 16 optimal weight: 2.9990 chunk 43 optimal weight: 20.0000 chunk 15 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 764 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 = 0.5124 r_free = 0.5124 target = 0.283351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.244082 restraints weight = 4519.512| |-----------------------------------------------------------------------------| r_work (start): 0.4835 rms_B_bonded: 2.12 r_work: 0.4733 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5156 moved from start: 0.4509 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= 0.139 Angle : 0.638 6.650 6017 Z= 0.326 Chirality : 0.043 0.200 707 Planarity : 0.004 0.041 635 Dihedral : 20.705 150.927 1039 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 2.77 % Allowed : 32.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.42), residues: 415 helix: 0.90 (0.45), residues: 142 sheet: -1.20 (0.52), residues: 82 loop : -0.95 (0.48), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 435 HIS 0.006 0.001 HIS A 764 PHE 0.027 0.002 PHE A 811 TYR 0.015 0.002 TYR A 667 ARG 0.003 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04931 ( 153) hydrogen bonds : angle 5.23398 ( 399) covalent geometry : bond 0.00315 ( 4307) covalent geometry : angle 0.63767 ( 6017) *********************** 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 50 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 1.128 Fit side-chains REVERT: A 505 PHE cc_start: 0.5654 (OUTLIER) cc_final: 0.4929 (t80) REVERT: A 516 GLN cc_start: 0.7213 (OUTLIER) cc_final: 0.6926 (pt0) REVERT: A 542 MET cc_start: 0.5796 (pmm) cc_final: 0.5238 (ptp) REVERT: A 548 GLN cc_start: 0.5676 (OUTLIER) cc_final: 0.5389 (mt0) REVERT: A 576 ASN cc_start: 0.6992 (p0) cc_final: 0.6680 (p0) REVERT: A 710 ARG cc_start: 0.4227 (tmt90) cc_final: 0.2597 (tmt-80) outliers start: 10 outliers final: 4 residues processed: 49 average time/residue: 1.4827 time to fit residues: 75.4823 Evaluate side-chains 45 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 516 GLN Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 586 VAL 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 4 optimal weight: 5.9990 chunk 23 optimal weight: 0.0980 chunk 0 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 764 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 = 0.5109 r_free = 0.5109 target = 0.283810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.243100 restraints weight = 4549.637| |-----------------------------------------------------------------------------| r_work (start): 0.4817 rms_B_bonded: 2.15 r_work: 0.4718 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5169 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4307 Z= 0.153 Angle : 0.653 6.624 6017 Z= 0.334 Chirality : 0.044 0.201 707 Planarity : 0.005 0.043 635 Dihedral : 20.688 151.007 1039 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.23 % Favored : 92.53 % Rotamer: Outliers : 3.88 % Allowed : 31.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.42), residues: 415 helix: 0.91 (0.45), residues: 141 sheet: -1.35 (0.48), residues: 92 loop : -0.84 (0.50), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 769 HIS 0.008 0.001 HIS A 839 PHE 0.025 0.002 PHE A 811 TYR 0.024 0.002 TYR A 784 ARG 0.002 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.05180 ( 153) hydrogen bonds : angle 5.25668 ( 399) covalent geometry : bond 0.00350 ( 4307) covalent geometry : angle 0.65250 ( 6017) ********************** 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: 14 poor density : 43 time to evaluate : 0.392 Fit side-chains REVERT: A 437 MET cc_start: 0.4437 (ttp) cc_final: 0.4128 (tpt) REVERT: A 505 PHE cc_start: 0.5499 (OUTLIER) cc_final: 0.4680 (t80) REVERT: A 516 GLN cc_start: 0.7125 (OUTLIER) cc_final: 0.6861 (pt0) REVERT: A 542 MET cc_start: 0.5847 (pmm) cc_final: 0.5288 (ptp) REVERT: A 548 GLN cc_start: 0.5751 (OUTLIER) cc_final: 0.5502 (mt0) REVERT: A 576 ASN cc_start: 0.7038 (p0) cc_final: 0.6696 (p0) REVERT: A 710 ARG cc_start: 0.4253 (tmt90) cc_final: 0.2599 (tmt-80) outliers start: 14 outliers final: 6 residues processed: 55 average time/residue: 1.0822 time to fit residues: 62.0281 Evaluate side-chains 48 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 516 GLN 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 586 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 781 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 0.0570 chunk 34 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 11 optimal weight: 0.3980 chunk 31 optimal weight: 0.0000 chunk 27 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 overall best weight: 0.2902 ------------------------------------------------------------------------------- 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 ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5145 r_free = 0.5145 target = 0.284482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.247030 restraints weight = 4516.716| |-----------------------------------------------------------------------------| r_work (start): 0.4838 rms_B_bonded: 2.02 r_work: 0.4707 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5216 moved from start: 0.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4307 Z= 0.126 Angle : 0.633 8.012 6017 Z= 0.322 Chirality : 0.043 0.201 707 Planarity : 0.004 0.040 635 Dihedral : 20.619 152.116 1039 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.05 % Allowed : 32.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.42), residues: 415 helix: 1.02 (0.46), residues: 141 sheet: -1.31 (0.51), residues: 82 loop : -1.04 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 451 HIS 0.011 0.002 HIS A 764 PHE 0.021 0.002 PHE A 811 TYR 0.014 0.002 TYR A 667 ARG 0.003 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04682 ( 153) hydrogen bonds : angle 5.09643 ( 399) covalent geometry : bond 0.00289 ( 4307) covalent geometry : angle 0.63310 ( 6017) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3344.24 seconds wall clock time: 58 minutes 55.15 seconds (3535.15 seconds total)