Starting phenix.real_space_refine on Wed Sep 17 04:25:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k6t_62135/09_2025/9k6t_62135.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k6t_62135/09_2025/9k6t_62135.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/9k6t_62135/09_2025/9k6t_62135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k6t_62135/09_2025/9k6t_62135.map" model { file = "/net/cci-nas-00/data/ceres_data/9k6t_62135/09_2025/9k6t_62135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k6t_62135/09_2025/9k6t_62135.cif" } 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= 0.043 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 42 5.49 5 Mg 1 5.21 5 S 19 5.16 5 C 2520 2.51 5 N 758 2.21 5 O 882 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 4222 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: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 441 Classifications: {'RNA': 21} Modifications used: {'p5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 11} Link IDs: {'rna2p': 2, 'rna3p': 18} Chain: "C" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 448 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 11, 'rna3p_pyr': 8} Link IDs: {'rna2p': 2, 'rna3p': 18} 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: 1.36, per 1000 atoms: 0.32 Number of scatterers: 4222 At special positions: 0 Unit cell: (67.26, 78.66, 98.04, 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 42 15.00 Mg 1 11.99 O 882 8.00 N 758 7.00 C 2520 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: 0.39 Conformation dependent library (CDL) restraints added in 141.5 milliseconds Enol-peptide restraints added in 476.8 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: 10 helices and 3 sheets defined 33.0% alpha, 13.8% beta 8 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 463 through 481 Processing helix chain 'A' and resid 501 through 510 Processing helix chain 'A' and resid 526 through 538 removed outlier: 4.361A pdb=" N ALA A 530 " --> pdb=" O THR A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 554 removed outlier: 3.765A pdb=" N GLN A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) removed outlier: 3.723A 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 571 Processing helix chain 'A' and resid 584 through 589 Processing helix chain 'A' and resid 641 through 658 Processing helix chain 'A' and resid 675 through 692 removed outlier: 3.590A pdb=" N VAL A 679 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 685 " --> pdb=" O HIS A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 789 Processing helix chain 'A' and resid 800 through 817 Processing sheet with id=AA1, first strand: chain 'A' and resid 411 through 412 removed outlier: 5.785A pdb=" N PHE A 666 " --> pdb=" O ILE A 705 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL A 707 " --> pdb=" O PHE A 666 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ARG A 668 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL A 598 " --> pdb=" O ALA A 669 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N PHE A 593 " --> pdb=" O SER A 617 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 418 through 419 Processing sheet with id=AA3, first strand: chain 'A' and resid 491 through 494 removed outlier: 3.910A pdb=" N PHE A 491 " --> pdb=" O TRP A 451 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ALA A 452 " --> pdb=" O VAL A 519 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ILE A 521 " --> pdb=" O ALA A 452 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA A 454 " --> pdb=" O ILE A 521 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL A 518 " --> pdb=" O GLN A 545 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N VAL A 547 " --> pdb=" O VAL A 518 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL A 520 " --> pdb=" O VAL A 547 " (cutoff:3.500A) 135 hydrogen bonds defined for protein. 378 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 19 hydrogen bonds 38 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 0.69 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 591 1.32 - 1.44: 1403 1.44 - 1.56: 2296 1.56 - 1.69: 84 1.69 - 1.81: 27 Bond restraints: 4401 Sorted by residual: bond pdb=" CG PRO A 700 " pdb=" CD PRO A 700 " ideal model delta sigma weight residual 1.503 1.338 0.165 3.40e-02 8.65e+02 2.36e+01 bond pdb=" CA LYS A 844 " pdb=" C LYS A 844 " ideal model delta sigma weight residual 1.521 1.474 0.047 1.27e-02 6.20e+03 1.36e+01 bond pdb=" N LEU A 817 " pdb=" CA LEU A 817 " ideal model delta sigma weight residual 1.463 1.418 0.045 1.31e-02 5.83e+03 1.17e+01 bond pdb=" CA ALA A 841 " pdb=" C ALA A 841 " ideal model delta sigma weight residual 1.526 1.486 0.040 1.23e-02 6.61e+03 1.07e+01 bond pdb=" N VAL A 707 " pdb=" CA VAL A 707 " ideal model delta sigma weight residual 1.458 1.492 -0.035 1.14e-02 7.69e+03 9.37e+00 ... (remaining 4396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 5919 2.81 - 5.62: 192 5.62 - 8.43: 43 8.43 - 11.23: 6 11.23 - 14.04: 3 Bond angle restraints: 6163 Sorted by residual: angle pdb=" N PRO A 700 " pdb=" CD PRO A 700 " pdb=" CG PRO A 700 " ideal model delta sigma weight residual 103.20 89.16 14.04 1.50e+00 4.44e-01 8.76e+01 angle pdb=" N LYS A 844 " pdb=" CA LYS A 844 " pdb=" C LYS A 844 " ideal model delta sigma weight residual 113.97 102.38 11.59 1.28e+00 6.10e-01 8.20e+01 angle pdb=" CA PRO A 700 " pdb=" N PRO A 700 " pdb=" CD PRO A 700 " ideal model delta sigma weight residual 112.00 102.54 9.46 1.40e+00 5.10e-01 4.57e+01 angle pdb=" CA PRO A 700 " pdb=" CB PRO A 700 " pdb=" CG PRO A 700 " ideal model delta sigma weight residual 104.50 93.11 11.39 1.90e+00 2.77e-01 3.59e+01 angle pdb=" N LEU A 768 " pdb=" CA LEU A 768 " pdb=" C LEU A 768 " ideal model delta sigma weight residual 113.55 106.31 7.24 1.26e+00 6.30e-01 3.30e+01 ... (remaining 6158 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 2461 35.84 - 71.69: 206 71.69 - 107.53: 20 107.53 - 143.37: 1 143.37 - 179.22: 3 Dihedral angle restraints: 2691 sinusoidal: 1469 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 -128.00 46.85 -174.85 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' C B 14 " pdb=" C1' C B 14 " pdb=" N1 C B 14 " pdb=" C2 C B 14 " ideal model delta sinusoidal sigma weight residual -160.00 -75.27 -84.73 1 1.50e+01 4.44e-03 3.87e+01 dihedral pdb=" O4' C C 6 " pdb=" C2' C C 6 " pdb=" C1' C C 6 " pdb=" C3' C C 6 " ideal model delta sinusoidal sigma weight residual 25.00 -15.05 40.05 1 8.00e+00 1.56e-02 3.52e+01 ... (remaining 2688 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 632 0.111 - 0.222: 69 0.222 - 0.332: 2 0.332 - 0.443: 11 0.443 - 0.554: 13 Chirality restraints: 727 Sorted by residual: chirality pdb=" P U B 1 " pdb=" OP1 U B 1 " pdb=" OP2 U B 1 " pdb=" O5' U B 1 " both_signs ideal model delta sigma weight residual True 2.41 2.96 -0.55 2.00e-01 2.50e+01 7.67e+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 -2.94 -0.53 2.00e-01 2.50e+01 7.04e+00 chirality pdb=" P A C 5 " pdb=" OP1 A C 5 " pdb=" OP2 A C 5 " pdb=" O5' A C 5 " both_signs ideal model delta sigma weight residual True 2.41 -2.94 -0.53 2.00e-01 2.50e+01 7.00e+00 ... (remaining 724 not shown) Planarity restraints: 639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 761 " -0.511 9.50e-02 1.11e+02 2.29e-01 3.21e+01 pdb=" NE ARG A 761 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARG A 761 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 761 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 761 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 816 " 0.024 2.00e-02 2.50e+03 4.71e-02 2.22e+01 pdb=" C HIS A 816 " -0.081 2.00e-02 2.50e+03 pdb=" O HIS A 816 " 0.030 2.00e-02 2.50e+03 pdb=" N LEU A 817 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 699 " 0.075 5.00e-02 4.00e+02 1.06e-01 1.81e+01 pdb=" N PRO A 700 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO A 700 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 700 " 0.057 5.00e-02 4.00e+02 ... (remaining 636 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 397 2.74 - 3.28: 3931 3.28 - 3.82: 7823 3.82 - 4.36: 8879 4.36 - 4.90: 14376 Nonbonded interactions: 35406 Sorted by model distance: nonbonded pdb=" O GLN A 785 " pdb=" OG1 THR A 789 " model vdw 2.197 3.040 nonbonded pdb=" OG SER A 752 " pdb=" O VAL A 797 " model vdw 2.217 3.040 nonbonded pdb=" OE1 GLN A 652 " pdb=" OG SER A 656 " model vdw 2.332 3.040 nonbonded pdb=" NE2 GLN A 632 " pdb=" O GLN A 636 " model vdw 2.378 3.120 nonbonded pdb=" O SER A 752 " pdb=" OG SER A 752 " model vdw 2.380 3.040 ... (remaining 35401 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: 0.290 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: 0.020 Process input model: 7.050 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:8.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6184 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 : 0.007 0.165 4401 Z= 0.414 Angle : 1.222 14.042 6163 Z= 0.688 Chirality : 0.105 0.554 727 Planarity : 0.013 0.229 639 Dihedral : 23.560 179.217 1903 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.72 % Allowed : 5.06 % Favored : 94.22 % Rotamer: Outliers : 3.32 % Allowed : 26.04 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.88 (0.39), residues: 415 helix: -0.99 (0.40), residues: 140 sheet: -1.62 (0.50), residues: 85 loop : -1.10 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 854 TYR 0.031 0.002 TYR A 805 PHE 0.024 0.003 PHE A 653 TRP 0.013 0.002 TRP A 435 HIS 0.011 0.002 HIS A 682 Details of bonding type rmsd covalent geometry : bond 0.00750 ( 4401) covalent geometry : angle 1.22205 ( 6163) hydrogen bonds : bond 0.15165 ( 154) hydrogen bonds : angle 7.82008 ( 416) *********************** 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 56 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.143 Fit side-chains REVERT: A 761 ARG cc_start: 0.4986 (OUTLIER) cc_final: 0.4060 (mmt-90) REVERT: A 844 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7812 (mtmt) outliers start: 12 outliers final: 3 residues processed: 54 average time/residue: 0.7730 time to fit residues: 43.0530 Evaluate side-chains 41 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 761 ARG Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 769 TRP Chi-restraints excluded: chain A residue 838 ASP Chi-restraints excluded: chain A residue 844 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.0040 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 GLN ** A 682 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 = 0.4770 r_free = 0.4770 target = 0.253527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.199018 restraints weight = 4832.561| |-----------------------------------------------------------------------------| r_work (start): 0.4336 rms_B_bonded: 2.52 r_work: 0.4229 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5800 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4401 Z= 0.151 Angle : 0.706 7.449 6163 Z= 0.364 Chirality : 0.047 0.226 727 Planarity : 0.006 0.062 639 Dihedral : 23.685 174.573 1109 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 5.54 % Allowed : 26.32 % Favored : 68.14 % 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: -1.14 (0.41), residues: 415 helix: 0.12 (0.44), residues: 140 sheet: -1.52 (0.50), residues: 85 loop : -0.93 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 583 TYR 0.020 0.001 TYR A 765 PHE 0.016 0.002 PHE A 653 TRP 0.009 0.002 TRP A 435 HIS 0.010 0.002 HIS A 807 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 4401) covalent geometry : angle 0.70586 ( 6163) hydrogen bonds : bond 0.04387 ( 154) hydrogen bonds : angle 5.57590 ( 416) *********************** 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 65 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 45 time to evaluate : 0.144 Fit side-chains REVERT: A 447 GLU cc_start: 0.6255 (tm-30) cc_final: 0.5982 (tm-30) REVERT: A 549 MET cc_start: 0.5078 (tpp) cc_final: 0.4307 (ptm) REVERT: A 804 TYR cc_start: 0.7257 (OUTLIER) cc_final: 0.6289 (m-80) outliers start: 20 outliers final: 6 residues processed: 61 average time/residue: 0.4532 time to fit residues: 29.0513 Evaluate side-chains 48 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 769 TRP Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 838 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 2 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 33 optimal weight: 9.9990 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 780 GLN A 807 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.257076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.203541 restraints weight = 4780.944| |-----------------------------------------------------------------------------| r_work (start): 0.4354 rms_B_bonded: 2.48 r_work: 0.4247 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5810 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4401 Z= 0.135 Angle : 0.645 6.544 6163 Z= 0.337 Chirality : 0.046 0.223 727 Planarity : 0.005 0.044 639 Dihedral : 23.257 173.117 1101 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.43 % Allowed : 30.19 % 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: -0.90 (0.42), residues: 415 helix: 0.41 (0.44), residues: 139 sheet: -1.54 (0.49), residues: 89 loop : -0.75 (0.49), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 688 TYR 0.012 0.001 TYR A 765 PHE 0.016 0.002 PHE A 653 TRP 0.006 0.001 TRP A 435 HIS 0.009 0.001 HIS A 807 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 4401) covalent geometry : angle 0.64479 ( 6163) hydrogen bonds : bond 0.04402 ( 154) hydrogen bonds : angle 5.34425 ( 416) *********************** 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 58 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.095 Fit side-chains REVERT: A 447 GLU cc_start: 0.6159 (tm-30) cc_final: 0.5856 (tm-30) REVERT: A 549 MET cc_start: 0.5329 (tpp) cc_final: 0.4326 (ptm) REVERT: A 804 TYR cc_start: 0.7195 (OUTLIER) cc_final: 0.6355 (m-80) outliers start: 16 outliers final: 7 residues processed: 53 average time/residue: 0.4175 time to fit residues: 23.2886 Evaluate side-chains 45 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 769 TRP Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain A residue 838 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 24 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 41 optimal weight: 0.1980 chunk 12 optimal weight: 0.6980 chunk 1 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.250884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.195788 restraints weight = 4770.799| |-----------------------------------------------------------------------------| r_work (start): 0.4314 rms_B_bonded: 2.48 r_work: 0.4208 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5869 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4401 Z= 0.155 Angle : 0.660 7.089 6163 Z= 0.342 Chirality : 0.047 0.218 727 Planarity : 0.005 0.044 639 Dihedral : 23.054 171.280 1099 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.43 % Allowed : 31.86 % Favored : 63.71 % 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: -0.78 (0.42), residues: 415 helix: 0.53 (0.44), residues: 139 sheet: -1.38 (0.51), residues: 89 loop : -0.74 (0.50), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 812 TYR 0.014 0.001 TYR A 765 PHE 0.015 0.002 PHE A 653 TRP 0.007 0.001 TRP A 435 HIS 0.006 0.001 HIS A 807 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 4401) covalent geometry : angle 0.65992 ( 6163) hydrogen bonds : bond 0.04293 ( 154) hydrogen bonds : angle 5.41233 ( 416) *********************** 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 57 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.169 Fit side-chains REVERT: A 447 GLU cc_start: 0.6272 (tm-30) cc_final: 0.5935 (tm-30) REVERT: A 549 MET cc_start: 0.5444 (tpp) cc_final: 0.4392 (ptm) REVERT: A 607 LYS cc_start: 0.6577 (OUTLIER) cc_final: 0.6323 (mtmm) REVERT: A 804 TYR cc_start: 0.7156 (OUTLIER) cc_final: 0.6128 (m-80) outliers start: 16 outliers final: 9 residues processed: 53 average time/residue: 0.5087 time to fit residues: 28.1186 Evaluate side-chains 46 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 607 LYS Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 769 TRP Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 838 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 30 optimal weight: 8.9990 chunk 22 optimal weight: 0.1980 chunk 13 optimal weight: 0.6980 chunk 1 optimal weight: 0.0770 chunk 6 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 37 optimal weight: 0.1980 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 ASN ** A 682 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.259282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.205724 restraints weight = 4758.809| |-----------------------------------------------------------------------------| r_work (start): 0.4373 rms_B_bonded: 2.47 r_work: 0.4272 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5768 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4401 Z= 0.118 Angle : 0.612 6.278 6163 Z= 0.321 Chirality : 0.045 0.215 727 Planarity : 0.005 0.043 639 Dihedral : 22.801 173.425 1099 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 6.93 % Allowed : 30.19 % Favored : 62.88 % 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: -0.67 (0.43), residues: 415 helix: 0.79 (0.44), residues: 139 sheet: -1.44 (0.51), residues: 94 loop : -0.74 (0.50), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 663 TYR 0.009 0.001 TYR A 804 PHE 0.014 0.001 PHE A 659 TRP 0.007 0.001 TRP A 769 HIS 0.006 0.001 HIS A 807 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 4401) covalent geometry : angle 0.61165 ( 6163) hydrogen bonds : bond 0.03968 ( 154) hydrogen bonds : angle 5.18252 ( 416) *********************** 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 64 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 39 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: A 468 LYS cc_start: 0.6396 (mmmm) cc_final: 0.5943 (mmtt) REVERT: A 549 MET cc_start: 0.5380 (tpp) cc_final: 0.4557 (ptm) REVERT: A 607 LYS cc_start: 0.6556 (OUTLIER) cc_final: 0.6295 (mtmm) REVERT: A 804 TYR cc_start: 0.7498 (OUTLIER) cc_final: 0.6354 (m-80) outliers start: 25 outliers final: 8 residues processed: 59 average time/residue: 0.4254 time to fit residues: 26.2222 Evaluate side-chains 49 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 607 LYS Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 769 TRP Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain A residue 838 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 11 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 43 optimal weight: 20.0000 chunk 14 optimal weight: 0.2980 chunk 2 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 0.0010 chunk 17 optimal weight: 0.0050 chunk 35 optimal weight: 0.3980 chunk 3 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.259804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.205641 restraints weight = 4832.193| |-----------------------------------------------------------------------------| r_work (start): 0.4372 rms_B_bonded: 2.50 r_work: 0.4271 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5765 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4401 Z= 0.117 Angle : 0.608 6.258 6163 Z= 0.316 Chirality : 0.044 0.211 727 Planarity : 0.005 0.042 639 Dihedral : 22.679 173.914 1099 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.71 % Allowed : 31.02 % Favored : 64.27 % 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: -0.56 (0.43), residues: 415 helix: 0.90 (0.45), residues: 139 sheet: -1.40 (0.51), residues: 94 loop : -0.67 (0.50), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 663 TYR 0.018 0.001 TYR A 765 PHE 0.013 0.001 PHE A 653 TRP 0.008 0.001 TRP A 769 HIS 0.011 0.001 HIS A 807 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 4401) covalent geometry : angle 0.60781 ( 6163) hydrogen bonds : bond 0.03994 ( 154) hydrogen bonds : angle 5.15005 ( 416) *********************** 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 56 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 39 time to evaluate : 0.105 Fit side-chains revert: symmetry clash REVERT: A 468 LYS cc_start: 0.6379 (mmmm) cc_final: 0.5920 (mmtt) REVERT: A 549 MET cc_start: 0.5461 (tpp) cc_final: 0.4623 (ptm) REVERT: A 607 LYS cc_start: 0.6554 (OUTLIER) cc_final: 0.6290 (mtmm) REVERT: A 767 VAL cc_start: 0.4445 (OUTLIER) cc_final: 0.4138 (p) REVERT: A 804 TYR cc_start: 0.7460 (OUTLIER) cc_final: 0.6262 (m-80) outliers start: 17 outliers final: 6 residues processed: 53 average time/residue: 0.4783 time to fit residues: 26.4783 Evaluate side-chains 45 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 607 LYS Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 769 TRP Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 838 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 42 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 ASN ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 699 GLN A 753 HIS ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.243090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.187651 restraints weight = 4903.417| |-----------------------------------------------------------------------------| r_work (start): 0.4192 rms_B_bonded: 2.48 r_work: 0.4082 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6002 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 4401 Z= 0.283 Angle : 0.802 9.093 6163 Z= 0.409 Chirality : 0.051 0.209 727 Planarity : 0.006 0.054 639 Dihedral : 22.978 165.789 1099 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 6.09 % Allowed : 30.19 % Favored : 63.71 % 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: -1.03 (0.42), residues: 415 helix: -0.06 (0.42), residues: 140 sheet: -1.29 (0.52), residues: 98 loop : -0.64 (0.52), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 812 TYR 0.040 0.003 TYR A 765 PHE 0.021 0.003 PHE A 659 TRP 0.011 0.002 TRP A 435 HIS 0.005 0.002 HIS A 839 Details of bonding type rmsd covalent geometry : bond 0.00683 ( 4401) covalent geometry : angle 0.80226 ( 6163) hydrogen bonds : bond 0.05797 ( 154) hydrogen bonds : angle 5.73840 ( 416) *********************** 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 62 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 40 time to evaluate : 0.145 Fit side-chains REVERT: A 468 LYS cc_start: 0.6417 (mmmm) cc_final: 0.5976 (mmtt) REVERT: A 607 LYS cc_start: 0.6676 (OUTLIER) cc_final: 0.6400 (mmmt) REVERT: A 705 ILE cc_start: 0.7460 (mt) cc_final: 0.7204 (mp) REVERT: A 804 TYR cc_start: 0.7385 (OUTLIER) cc_final: 0.6465 (m-80) outliers start: 22 outliers final: 12 residues processed: 55 average time/residue: 0.5154 time to fit residues: 29.5502 Evaluate side-chains 55 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 607 LYS Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 769 TRP Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 838 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 11 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 43 optimal weight: 20.0000 chunk 0 optimal weight: 3.9990 chunk 22 optimal weight: 0.1980 chunk 8 optimal weight: 3.9990 chunk 44 optimal weight: 20.0000 chunk 20 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 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 459 GLN A 699 GLN ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.249888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.195486 restraints weight = 4809.517| |-----------------------------------------------------------------------------| r_work (start): 0.4302 rms_B_bonded: 2.44 r_work: 0.4198 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5885 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4401 Z= 0.149 Angle : 0.682 11.143 6163 Z= 0.351 Chirality : 0.046 0.211 727 Planarity : 0.005 0.069 639 Dihedral : 22.781 168.178 1099 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.99 % Allowed : 32.13 % Favored : 62.88 % 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: -0.82 (0.42), residues: 415 helix: 0.38 (0.43), residues: 140 sheet: -1.42 (0.50), residues: 89 loop : -0.66 (0.50), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 663 TYR 0.018 0.001 TYR A 765 PHE 0.017 0.002 PHE A 659 TRP 0.008 0.001 TRP A 769 HIS 0.007 0.001 HIS A 807 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 4401) covalent geometry : angle 0.68216 ( 6163) hydrogen bonds : bond 0.04541 ( 154) hydrogen bonds : angle 5.40699 ( 416) *********************** 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 59 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 41 time to evaluate : 0.112 Fit side-chains REVERT: A 429 THR cc_start: 0.7845 (p) cc_final: 0.7565 (p) REVERT: A 468 LYS cc_start: 0.6390 (mmmm) cc_final: 0.6006 (mmtt) REVERT: A 549 MET cc_start: 0.5230 (tpp) cc_final: 0.4407 (ptm) REVERT: A 586 VAL cc_start: 0.6079 (t) cc_final: 0.5806 (t) REVERT: A 607 LYS cc_start: 0.6619 (OUTLIER) cc_final: 0.6333 (mmmt) REVERT: A 767 VAL cc_start: 0.4497 (OUTLIER) cc_final: 0.4196 (p) REVERT: A 804 TYR cc_start: 0.7558 (OUTLIER) cc_final: 0.6582 (m-80) outliers start: 18 outliers final: 12 residues processed: 55 average time/residue: 0.5259 time to fit residues: 30.0733 Evaluate side-chains 52 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 37 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 607 LYS Chi-restraints excluded: chain A residue 699 GLN Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 769 TRP Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain A residue 838 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 GLN ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.253222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.199017 restraints weight = 4799.397| |-----------------------------------------------------------------------------| r_work (start): 0.4303 rms_B_bonded: 2.46 r_work: 0.4199 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5899 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4401 Z= 0.150 Angle : 0.681 10.712 6163 Z= 0.351 Chirality : 0.046 0.211 727 Planarity : 0.005 0.080 639 Dihedral : 22.722 168.854 1099 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.43 % Allowed : 32.96 % Favored : 62.60 % 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: -0.86 (0.42), residues: 415 helix: 0.44 (0.43), residues: 139 sheet: -1.39 (0.51), residues: 94 loop : -0.76 (0.50), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 663 TYR 0.018 0.002 TYR A 765 PHE 0.015 0.002 PHE A 659 TRP 0.008 0.001 TRP A 769 HIS 0.013 0.001 HIS A 807 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 4401) covalent geometry : angle 0.68142 ( 6163) hydrogen bonds : bond 0.04554 ( 154) hydrogen bonds : angle 5.41873 ( 416) *********************** 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 55 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.148 Fit side-chains REVERT: A 429 THR cc_start: 0.7832 (p) cc_final: 0.7553 (p) REVERT: A 468 LYS cc_start: 0.6348 (mmmm) cc_final: 0.5990 (mmtt) REVERT: A 483 MET cc_start: 0.7220 (ttp) cc_final: 0.6882 (ttp) REVERT: A 549 MET cc_start: 0.5307 (tpp) cc_final: 0.4468 (ptm) REVERT: A 586 VAL cc_start: 0.6322 (t) cc_final: 0.6103 (t) REVERT: A 607 LYS cc_start: 0.6622 (OUTLIER) cc_final: 0.6333 (mmmt) REVERT: A 804 TYR cc_start: 0.7406 (OUTLIER) cc_final: 0.6544 (m-80) outliers start: 16 outliers final: 13 residues processed: 52 average time/residue: 0.4818 time to fit residues: 26.1953 Evaluate side-chains 52 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 37 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 607 LYS Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 769 TRP Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain A residue 838 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 2 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN A 459 GLN ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4803 r_free = 0.4803 target = 0.253838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.199634 restraints weight = 4784.874| |-----------------------------------------------------------------------------| r_work (start): 0.4310 rms_B_bonded: 2.46 r_work: 0.4206 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5873 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4401 Z= 0.149 Angle : 0.678 10.447 6163 Z= 0.347 Chirality : 0.046 0.210 727 Planarity : 0.006 0.082 639 Dihedral : 22.685 169.497 1099 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.43 % Allowed : 32.69 % Favored : 62.88 % 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: -0.88 (0.42), residues: 415 helix: 0.39 (0.44), residues: 139 sheet: -1.40 (0.51), residues: 94 loop : -0.76 (0.50), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 663 TYR 0.017 0.001 TYR A 765 PHE 0.015 0.002 PHE A 659 TRP 0.008 0.001 TRP A 769 HIS 0.016 0.002 HIS A 807 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 4401) covalent geometry : angle 0.67782 ( 6163) hydrogen bonds : bond 0.04545 ( 154) hydrogen bonds : angle 5.41521 ( 416) ********************** 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 54 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 0.157 Fit side-chains REVERT: A 429 THR cc_start: 0.7839 (p) cc_final: 0.7561 (p) REVERT: A 448 ILE cc_start: 0.6509 (OUTLIER) cc_final: 0.6117 (mm) REVERT: A 468 LYS cc_start: 0.6263 (mmmm) cc_final: 0.5915 (mmtt) REVERT: A 483 MET cc_start: 0.7165 (ttp) cc_final: 0.6844 (ttp) REVERT: A 549 MET cc_start: 0.5230 (tpp) cc_final: 0.4389 (ptm) REVERT: A 586 VAL cc_start: 0.6242 (t) cc_final: 0.5992 (t) REVERT: A 607 LYS cc_start: 0.6627 (OUTLIER) cc_final: 0.6329 (mmmt) REVERT: A 804 TYR cc_start: 0.7390 (OUTLIER) cc_final: 0.6357 (m-80) REVERT: A 811 PHE cc_start: 0.7241 (m-80) cc_final: 0.6697 (m-80) outliers start: 16 outliers final: 13 residues processed: 50 average time/residue: 0.4989 time to fit residues: 26.0555 Evaluate side-chains 52 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 36 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 607 LYS Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 769 TRP Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain A residue 838 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 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 459 GLN ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.254458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.200386 restraints weight = 4804.682| |-----------------------------------------------------------------------------| r_work (start): 0.4313 rms_B_bonded: 2.46 r_work: 0.4210 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5874 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4401 Z= 0.145 Angle : 0.671 10.173 6163 Z= 0.345 Chirality : 0.045 0.209 727 Planarity : 0.005 0.082 639 Dihedral : 22.650 170.042 1099 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.43 % Allowed : 33.24 % Favored : 62.33 % 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: -0.87 (0.42), residues: 415 helix: 0.41 (0.44), residues: 139 sheet: -1.41 (0.51), residues: 94 loop : -0.75 (0.50), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 663 TYR 0.016 0.001 TYR A 765 PHE 0.014 0.002 PHE A 659 TRP 0.008 0.001 TRP A 769 HIS 0.015 0.002 HIS A 807 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 4401) covalent geometry : angle 0.67070 ( 6163) hydrogen bonds : bond 0.04502 ( 154) hydrogen bonds : angle 5.40716 ( 416) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1561.24 seconds wall clock time: 27 minutes 29.24 seconds (1649.24 seconds total)