Starting phenix.real_space_refine on Wed Jul 23 19:10:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k6t_62135/07_2025/9k6t_62135.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k6t_62135/07_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_62135/07_2025/9k6t_62135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k6t_62135/07_2025/9k6t_62135.map" model { file = "/net/cci-nas-00/data/ceres_data/9k6t_62135/07_2025/9k6t_62135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k6t_62135/07_2025/9k6t_62135.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= 0.043 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 3.16, per 1000 atoms: 0.75 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: 1.24 Conformation dependent library (CDL) restraints added in 388.7 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: 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: 1.50 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: 1.56 Time building geometry restraints manager: 1.36 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: 0.150 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.260 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:15.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.870 ------------------------------------------------------------------------------- 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 (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: -1.88 (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 TRP 0.013 0.002 TRP A 435 HIS 0.011 0.002 HIS A 682 PHE 0.024 0.003 PHE A 653 TYR 0.031 0.002 TYR A 805 ARG 0.004 0.001 ARG A 854 Details of bonding type rmsd hydrogen bonds : bond 0.15165 ( 154) hydrogen bonds : angle 7.82008 ( 416) covalent geometry : bond 0.00750 ( 4401) covalent geometry : angle 1.22205 ( 6163) *********************** 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 : 0.363 Fit side-chains REVERT: A 761 ARG cc_start: 0.4986 (OUTLIER) cc_final: 0.4003 (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: 1.4805 time to fit residues: 82.6424 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 : 0.416 ------------------------------------------------------------------------------- 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 38 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 19 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.253363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.199032 restraints weight = 4784.654| |-----------------------------------------------------------------------------| r_work (start): 0.4332 rms_B_bonded: 2.52 r_work: 0.4225 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5810 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4401 Z= 0.156 Angle : 0.703 7.996 6163 Z= 0.365 Chirality : 0.048 0.223 727 Planarity : 0.006 0.069 639 Dihedral : 23.694 174.617 1109 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 5.54 % Allowed : 26.04 % Favored : 68.42 % 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: -1.17 (0.41), residues: 415 helix: 0.09 (0.44), residues: 140 sheet: -1.55 (0.50), residues: 85 loop : -0.94 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 435 HIS 0.010 0.002 HIS A 807 PHE 0.016 0.002 PHE A 653 TYR 0.016 0.001 TYR A 765 ARG 0.003 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04410 ( 154) hydrogen bonds : angle 5.60922 ( 416) covalent geometry : bond 0.00331 ( 4401) covalent geometry : angle 0.70292 ( 6163) *********************** 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 : 0.433 Fit side-chains REVERT: A 447 GLU cc_start: 0.6260 (tm-30) cc_final: 0.5988 (tm-30) REVERT: A 549 MET cc_start: 0.5268 (tpp) cc_final: 0.4313 (ptm) REVERT: A 804 TYR cc_start: 0.7260 (OUTLIER) cc_final: 0.6301 (m-80) outliers start: 20 outliers final: 6 residues processed: 61 average time/residue: 0.9883 time to fit residues: 63.0641 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 : 0.367 ------------------------------------------------------------------------------- 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 27 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 4 optimal weight: 0.0670 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4769 r_free = 0.4769 target = 0.253180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.198289 restraints weight = 4743.851| |-----------------------------------------------------------------------------| r_work (start): 0.4330 rms_B_bonded: 2.52 r_work: 0.4221 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5865 moved from start: 0.2056 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= 0.140 Angle : 0.651 7.212 6163 Z= 0.340 Chirality : 0.047 0.225 727 Planarity : 0.005 0.046 639 Dihedral : 23.293 172.751 1101 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 12.06 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 (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: -0.92 (0.42), residues: 415 helix: 0.43 (0.44), residues: 139 sheet: -1.58 (0.49), residues: 89 loop : -0.77 (0.49), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 435 HIS 0.008 0.001 HIS A 807 PHE 0.016 0.002 PHE A 653 TYR 0.010 0.001 TYR A 765 ARG 0.003 0.000 ARG A 688 Details of bonding type rmsd hydrogen bonds : bond 0.04367 ( 154) hydrogen bonds : angle 5.37729 ( 416) covalent geometry : bond 0.00307 ( 4401) covalent geometry : angle 0.65056 ( 6163) *********************** 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 57 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.364 Fit side-chains REVERT: A 447 GLU cc_start: 0.6171 (tm-30) cc_final: 0.5832 (tm-30) REVERT: A 549 MET cc_start: 0.5388 (tpp) cc_final: 0.4396 (ptm) REVERT: A 804 TYR cc_start: 0.7244 (OUTLIER) cc_final: 0.6332 (m-80) outliers start: 16 outliers final: 8 residues processed: 54 average time/residue: 0.8477 time to fit residues: 48.5482 Evaluate side-chains 50 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 556 THR 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 36 optimal weight: 3.9990 chunk 40 optimal weight: 0.0770 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 26 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 43 optimal weight: 20.0000 chunk 15 optimal weight: 4.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 682 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 HIS ** A 839 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.253644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.198789 restraints weight = 4819.157| |-----------------------------------------------------------------------------| r_work (start): 0.4346 rms_B_bonded: 2.52 r_work: 0.4242 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5812 moved from start: 0.2315 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= 0.132 Angle : 0.627 6.246 6163 Z= 0.327 Chirality : 0.046 0.219 727 Planarity : 0.005 0.046 639 Dihedral : 23.057 172.647 1099 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.99 % Allowed : 30.75 % 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 (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: -0.72 (0.43), residues: 415 helix: 0.71 (0.45), residues: 139 sheet: -1.51 (0.50), residues: 89 loop : -0.73 (0.50), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 435 HIS 0.006 0.001 HIS A 766 PHE 0.015 0.001 PHE A 653 TYR 0.012 0.001 TYR A 765 ARG 0.002 0.000 ARG A 854 Details of bonding type rmsd hydrogen bonds : bond 0.04087 ( 154) hydrogen bonds : angle 5.31335 ( 416) covalent geometry : bond 0.00289 ( 4401) covalent geometry : angle 0.62744 ( 6163) *********************** 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 59 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 41 time to evaluate : 0.424 Fit side-chains REVERT: A 447 GLU cc_start: 0.6198 (tm-30) cc_final: 0.5868 (tm-30) REVERT: A 472 GLU cc_start: 0.6297 (tm-30) cc_final: 0.5215 (mm-30) REVERT: A 483 MET cc_start: 0.7152 (ttp) cc_final: 0.6803 (ttp) REVERT: A 549 MET cc_start: 0.5338 (tpp) cc_final: 0.4323 (ptm) REVERT: A 804 TYR cc_start: 0.7472 (OUTLIER) cc_final: 0.6241 (m-80) outliers start: 18 outliers final: 7 residues processed: 54 average time/residue: 1.4372 time to fit residues: 80.4473 Evaluate side-chains 43 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 20 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 16 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 839 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.250379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.194435 restraints weight = 4859.714| |-----------------------------------------------------------------------------| r_work (start): 0.4290 rms_B_bonded: 2.53 r_work: 0.4181 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5933 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4401 Z= 0.165 Angle : 0.665 6.989 6163 Z= 0.343 Chirality : 0.046 0.218 727 Planarity : 0.005 0.042 639 Dihedral : 22.923 170.630 1099 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 6.65 % Allowed : 30.47 % 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 (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: -0.73 (0.43), residues: 415 helix: 0.59 (0.44), residues: 139 sheet: -1.54 (0.51), residues: 89 loop : -0.63 (0.51), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 435 HIS 0.007 0.001 HIS A 807 PHE 0.015 0.002 PHE A 659 TYR 0.017 0.002 TYR A 765 ARG 0.003 0.000 ARG A 812 Details of bonding type rmsd hydrogen bonds : bond 0.04463 ( 154) hydrogen bonds : angle 5.40359 ( 416) covalent geometry : bond 0.00380 ( 4401) covalent geometry : angle 0.66465 ( 6163) *********************** 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 67 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 43 time to evaluate : 0.410 Fit side-chains REVERT: A 447 GLU cc_start: 0.6187 (tm-30) cc_final: 0.5832 (tm-30) REVERT: A 468 LYS cc_start: 0.6472 (mmmm) cc_final: 0.5671 (mmtt) REVERT: A 472 GLU cc_start: 0.6397 (tm-30) cc_final: 0.5327 (mm-30) REVERT: A 549 MET cc_start: 0.5540 (tpp) cc_final: 0.4454 (ptm) REVERT: A 804 TYR cc_start: 0.7217 (OUTLIER) cc_final: 0.6202 (m-80) outliers start: 24 outliers final: 14 residues processed: 58 average time/residue: 0.9731 time to fit residues: 59.4591 Evaluate side-chains 55 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 586 VAL Chi-restraints excluded: chain A residue 591 VAL 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 768 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 0.0670 chunk 5 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 GLN ** A 682 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 = 0.4826 r_free = 0.4826 target = 0.257857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.203759 restraints weight = 4848.976| |-----------------------------------------------------------------------------| r_work (start): 0.4349 rms_B_bonded: 2.50 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: 0.5818 moved from start: 0.2845 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= 0.125 Angle : 0.620 6.843 6163 Z= 0.323 Chirality : 0.045 0.211 727 Planarity : 0.004 0.041 639 Dihedral : 22.739 172.485 1099 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 5.26 % Allowed : 31.58 % Favored : 63.16 % 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 (0.43), residues: 415 helix: 0.78 (0.44), residues: 139 sheet: -1.49 (0.51), residues: 94 loop : -0.65 (0.51), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 769 HIS 0.007 0.001 HIS A 807 PHE 0.014 0.001 PHE A 659 TYR 0.009 0.001 TYR A 804 ARG 0.002 0.000 ARG A 423 Details of bonding type rmsd hydrogen bonds : bond 0.04063 ( 154) hydrogen bonds : angle 5.20618 ( 416) covalent geometry : bond 0.00277 ( 4401) covalent geometry : angle 0.61988 ( 6163) *********************** 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 : 0.370 Fit side-chains REVERT: A 429 THR cc_start: 0.7704 (p) cc_final: 0.7447 (p) REVERT: A 468 LYS cc_start: 0.6408 (mmmm) cc_final: 0.5982 (mmtt) REVERT: A 483 MET cc_start: 0.7099 (ttp) cc_final: 0.6767 (ttp) REVERT: A 549 MET cc_start: 0.5489 (tpp) cc_final: 0.4553 (ptm) REVERT: A 804 TYR cc_start: 0.7464 (OUTLIER) cc_final: 0.6384 (m-80) outliers start: 19 outliers final: 11 residues processed: 53 average time/residue: 0.8261 time to fit residues: 46.4297 Evaluate side-chains 44 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 469 SER Chi-restraints excluded: chain A residue 591 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 7 optimal weight: 0.0970 chunk 16 optimal weight: 2.9990 chunk 44 optimal weight: 20.0000 chunk 29 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 807 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.251921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.197039 restraints weight = 4779.846| |-----------------------------------------------------------------------------| r_work (start): 0.4311 rms_B_bonded: 2.44 r_work: 0.4208 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5874 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4401 Z= 0.158 Angle : 0.650 6.651 6163 Z= 0.337 Chirality : 0.046 0.211 727 Planarity : 0.005 0.053 639 Dihedral : 22.744 171.188 1099 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 6.09 % Allowed : 30.47 % Favored : 63.43 % 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: -0.75 (0.43), residues: 415 helix: 0.61 (0.44), residues: 139 sheet: -1.49 (0.51), residues: 94 loop : -0.68 (0.51), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 769 HIS 0.014 0.001 HIS A 807 PHE 0.016 0.002 PHE A 659 TYR 0.013 0.001 TYR A 765 ARG 0.005 0.000 ARG A 663 Details of bonding type rmsd hydrogen bonds : bond 0.04520 ( 154) hydrogen bonds : angle 5.31671 ( 416) covalent geometry : bond 0.00366 ( 4401) covalent geometry : angle 0.65035 ( 6163) *********************** 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 60 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 38 time to evaluate : 0.447 Fit side-chains REVERT: A 468 LYS cc_start: 0.6383 (mmmm) cc_final: 0.5968 (mmtt) REVERT: A 483 MET cc_start: 0.7228 (ttp) cc_final: 0.6891 (ttp) REVERT: A 549 MET cc_start: 0.5631 (tpp) cc_final: 0.4596 (ptm) REVERT: A 804 TYR cc_start: 0.7438 (OUTLIER) cc_final: 0.6276 (m-80) outliers start: 22 outliers final: 15 residues processed: 55 average time/residue: 0.8850 time to fit residues: 51.3714 Evaluate side-chains 53 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 37 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 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 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 774 PHE Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 838 ASP Chi-restraints excluded: chain A residue 846 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 42 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 GLN A 753 HIS A 807 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.253318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.198301 restraints weight = 4756.640| |-----------------------------------------------------------------------------| r_work (start): 0.4332 rms_B_bonded: 2.44 r_work: 0.4231 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5848 moved from start: 0.3288 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= 0.139 Angle : 0.633 6.482 6163 Z= 0.330 Chirality : 0.045 0.207 727 Planarity : 0.005 0.069 639 Dihedral : 22.700 171.116 1099 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 5.54 % Allowed : 31.02 % Favored : 63.43 % 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: -0.72 (0.43), residues: 415 helix: 0.69 (0.44), residues: 139 sheet: -1.52 (0.50), residues: 96 loop : -0.66 (0.51), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 769 HIS 0.005 0.001 HIS A 807 PHE 0.016 0.002 PHE A 659 TYR 0.008 0.001 TYR A 765 ARG 0.002 0.000 ARG A 663 Details of bonding type rmsd hydrogen bonds : bond 0.04494 ( 154) hydrogen bonds : angle 5.27217 ( 416) covalent geometry : bond 0.00315 ( 4401) covalent geometry : angle 0.63316 ( 6163) *********************** 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 62 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 42 time to evaluate : 0.369 Fit side-chains REVERT: A 429 THR cc_start: 0.7747 (p) cc_final: 0.7471 (p) REVERT: A 468 LYS cc_start: 0.6341 (mmmm) cc_final: 0.5970 (mmtt) REVERT: A 504 MET cc_start: 0.5372 (ttt) cc_final: 0.5170 (ttp) REVERT: A 549 MET cc_start: 0.5521 (tpp) cc_final: 0.4523 (ptm) REVERT: A 767 VAL cc_start: 0.4340 (OUTLIER) cc_final: 0.4090 (p) REVERT: A 804 TYR cc_start: 0.7174 (OUTLIER) cc_final: 0.6104 (m-80) REVERT: A 811 PHE cc_start: 0.7433 (m-80) cc_final: 0.6772 (m-80) outliers start: 20 outliers final: 15 residues processed: 58 average time/residue: 1.0951 time to fit residues: 66.2973 Evaluate side-chains 53 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 36 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 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 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 774 PHE 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 Chi-restraints excluded: chain A residue 846 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 43 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 37 optimal weight: 0.0070 chunk 23 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 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 = 0.4823 r_free = 0.4823 target = 0.256503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.202098 restraints weight = 4795.077| |-----------------------------------------------------------------------------| r_work (start): 0.4329 rms_B_bonded: 2.46 r_work: 0.4227 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5868 moved from start: 0.3331 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= 0.137 Angle : 0.645 6.193 6163 Z= 0.334 Chirality : 0.045 0.207 727 Planarity : 0.005 0.073 639 Dihedral : 22.662 171.374 1099 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.43 % Allowed : 31.30 % 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 (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: -0.78 (0.43), residues: 415 helix: 0.69 (0.44), residues: 139 sheet: -1.57 (0.51), residues: 94 loop : -0.74 (0.51), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 769 HIS 0.013 0.001 HIS A 807 PHE 0.025 0.002 PHE A 811 TYR 0.009 0.001 TYR A 805 ARG 0.003 0.000 ARG A 812 Details of bonding type rmsd hydrogen bonds : bond 0.04429 ( 154) hydrogen bonds : angle 5.23899 ( 416) covalent geometry : bond 0.00310 ( 4401) covalent geometry : angle 0.64461 ( 6163) *********************** 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 54 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 0.609 Fit side-chains REVERT: A 429 THR cc_start: 0.7755 (p) cc_final: 0.7481 (p) REVERT: A 468 LYS cc_start: 0.6361 (mmmm) cc_final: 0.6001 (mmtt) REVERT: A 483 MET cc_start: 0.7111 (ttp) cc_final: 0.6798 (ttp) REVERT: A 549 MET cc_start: 0.5521 (tpp) cc_final: 0.4544 (ptm) REVERT: A 804 TYR cc_start: 0.7450 (OUTLIER) cc_final: 0.6176 (m-80) REVERT: A 811 PHE cc_start: 0.7493 (m-80) cc_final: 0.6779 (m-80) outliers start: 16 outliers final: 14 residues processed: 50 average time/residue: 1.5043 time to fit residues: 79.1709 Evaluate side-chains 53 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 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 735 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 769 TRP Chi-restraints excluded: chain A residue 774 PHE 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 25 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 807 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4808 r_free = 0.4808 target = 0.254621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.199972 restraints weight = 4753.151| |-----------------------------------------------------------------------------| r_work (start): 0.4308 rms_B_bonded: 2.45 r_work: 0.4205 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5885 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4401 Z= 0.158 Angle : 0.657 6.467 6163 Z= 0.338 Chirality : 0.046 0.207 727 Planarity : 0.005 0.074 639 Dihedral : 22.656 170.620 1099 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 5.26 % Allowed : 30.47 % 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 (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: -0.85 (0.43), residues: 415 helix: 0.54 (0.44), residues: 140 sheet: -1.60 (0.50), residues: 96 loop : -0.70 (0.51), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 769 HIS 0.018 0.001 HIS A 807 PHE 0.030 0.002 PHE A 811 TYR 0.009 0.001 TYR A 805 ARG 0.003 0.000 ARG A 812 Details of bonding type rmsd hydrogen bonds : bond 0.04607 ( 154) hydrogen bonds : angle 5.30872 ( 416) covalent geometry : bond 0.00365 ( 4401) covalent geometry : angle 0.65725 ( 6163) ********************** 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 56 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 37 time to evaluate : 1.050 Fit side-chains REVERT: A 468 LYS cc_start: 0.6375 (mmmm) cc_final: 0.5972 (mmtt) REVERT: A 483 MET cc_start: 0.7198 (ttp) cc_final: 0.6869 (ttp) REVERT: A 549 MET cc_start: 0.5579 (tpp) cc_final: 0.4569 (ptm) REVERT: A 767 VAL cc_start: 0.4475 (OUTLIER) cc_final: 0.4195 (p) REVERT: A 804 TYR cc_start: 0.7390 (OUTLIER) cc_final: 0.6185 (m-80) outliers start: 19 outliers final: 15 residues processed: 53 average time/residue: 2.0634 time to fit residues: 114.4833 Evaluate side-chains 52 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 35 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 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 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 774 PHE 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 Chi-restraints excluded: chain A residue 846 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 20.0000 chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 chunk 37 optimal weight: 0.0370 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 GLN ** A 780 GLN ** 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 = 0.4819 r_free = 0.4819 target = 0.256110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.201632 restraints weight = 4737.088| |-----------------------------------------------------------------------------| r_work (start): 0.4322 rms_B_bonded: 2.45 r_work: 0.4220 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5858 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4401 Z= 0.140 Angle : 0.660 7.207 6163 Z= 0.344 Chirality : 0.045 0.207 727 Planarity : 0.005 0.078 639 Dihedral : 22.619 171.315 1099 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.16 % Allowed : 31.58 % 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 (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: -0.81 (0.43), residues: 415 helix: 0.66 (0.44), residues: 139 sheet: -1.60 (0.51), residues: 94 loop : -0.75 (0.50), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 769 HIS 0.011 0.001 HIS A 807 PHE 0.016 0.001 PHE A 659 TYR 0.010 0.001 TYR A 804 ARG 0.002 0.000 ARG A 812 Details of bonding type rmsd hydrogen bonds : bond 0.04528 ( 154) hydrogen bonds : angle 5.33718 ( 416) covalent geometry : bond 0.00316 ( 4401) covalent geometry : angle 0.66011 ( 6163) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3611.92 seconds wall clock time: 67 minutes 25.54 seconds (4045.54 seconds total)