Starting phenix.real_space_refine on Fri May 9 14:59:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9knw_62464/05_2025/9knw_62464.cif Found real_map, /net/cci-nas-00/data/ceres_data/9knw_62464/05_2025/9knw_62464.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9knw_62464/05_2025/9knw_62464.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9knw_62464/05_2025/9knw_62464.map" model { file = "/net/cci-nas-00/data/ceres_data/9knw_62464/05_2025/9knw_62464.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9knw_62464/05_2025/9knw_62464.cif" } resolution = 3.41 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= 0.001 sd= 0.012 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 17 5.16 5 C 1783 2.51 5 N 460 2.21 5 O 484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 2747 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1000 Classifications: {'peptide': 126} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 118} Chain: "A" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 745 Classifications: {'peptide': 93} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 88} Chain: "C" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 879 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 89 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'PC8': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.86, per 1000 atoms: 1.04 Number of scatterers: 2747 At special positions: 0 Unit cell: (81.51, 93.48, 86.07, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 17 16.00 P 3 15.00 O 484 8.00 N 460 7.00 C 1783 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 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: 0.79 Conformation dependent library (CDL) restraints added in 314.6 milliseconds 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 614 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 2 sheets defined 60.4% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 28 through 33 Processing helix chain 'B' and resid 40 through 57 removed outlier: 3.789A pdb=" N TRP B 44 " --> pdb=" O THR B 40 " (cutoff:3.500A) Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 63 through 67 Processing helix chain 'B' and resid 68 through 86 Processing helix chain 'B' and resid 93 through 126 removed outlier: 3.688A pdb=" N HIS B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 23 removed outlier: 3.988A pdb=" N MET A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 29 removed outlier: 4.055A pdb=" N TRP A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 34 through 44 removed outlier: 3.521A pdb=" N ILE A 38 " --> pdb=" O TRP A 34 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 46 No H-bonds generated for 'chain 'A' and resid 45 through 46' Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.647A pdb=" N ILE A 50 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 73 Processing helix chain 'A' and resid 77 through 108 removed outlier: 3.695A pdb=" N PHE A 81 " --> pdb=" O ASN A 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.514A pdb=" N THR C 91 " --> pdb=" O PRO C 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.104A pdb=" N GLY C 10 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N SER C 114 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL C 12 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) 166 hydrogen bonds defined for protein. 465 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.70 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 409 1.30 - 1.43: 778 1.43 - 1.55: 1578 1.55 - 1.68: 20 1.68 - 1.81: 29 Bond restraints: 2814 Sorted by residual: bond pdb=" CB7 CDL B 201 " pdb=" OB8 CDL B 201 " ideal model delta sigma weight residual 1.334 1.436 -0.102 1.10e-02 8.26e+03 8.58e+01 bond pdb=" CA7 CDL B 201 " pdb=" OA8 CDL B 201 " ideal model delta sigma weight residual 1.334 1.430 -0.096 1.10e-02 8.26e+03 7.60e+01 bond pdb=" CA5 CDL B 201 " pdb=" OA6 CDL B 201 " ideal model delta sigma weight residual 1.342 1.440 -0.098 1.50e-02 4.44e+03 4.28e+01 bond pdb=" CB5 CDL B 201 " pdb=" OB6 CDL B 201 " ideal model delta sigma weight residual 1.342 1.438 -0.096 1.50e-02 4.44e+03 4.11e+01 bond pdb=" OB2 CDL B 201 " pdb=" PB2 CDL B 201 " ideal model delta sigma weight residual 1.579 1.664 -0.085 1.50e-02 4.44e+03 3.22e+01 ... (remaining 2809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 3736 3.13 - 6.25: 40 6.25 - 9.38: 8 9.38 - 12.51: 2 12.51 - 15.63: 1 Bond angle restraints: 3787 Sorted by residual: angle pdb=" C51 CDL B 201 " pdb=" CB5 CDL B 201 " pdb=" OB6 CDL B 201 " ideal model delta sigma weight residual 111.33 120.44 -9.11 1.32e+00 5.72e-01 4.75e+01 angle pdb=" C11 CDL B 201 " pdb=" CA5 CDL B 201 " pdb=" OA6 CDL B 201 " ideal model delta sigma weight residual 111.33 119.87 -8.54 1.32e+00 5.72e-01 4.17e+01 angle pdb=" C71 CDL B 201 " pdb=" CB7 CDL B 201 " pdb=" OB8 CDL B 201 " ideal model delta sigma weight residual 111.64 121.12 -9.48 1.65e+00 3.69e-01 3.32e+01 angle pdb=" CA2 CDL B 201 " pdb=" OA2 CDL B 201 " pdb=" PA1 CDL B 201 " ideal model delta sigma weight residual 121.27 115.75 5.52 1.00e+00 1.00e+00 3.05e+01 angle pdb=" C31 CDL B 201 " pdb=" CA7 CDL B 201 " pdb=" OA8 CDL B 201 " ideal model delta sigma weight residual 111.64 120.45 -8.81 1.65e+00 3.69e-01 2.86e+01 ... (remaining 3782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.66: 1562 29.66 - 59.32: 125 59.32 - 88.98: 5 88.98 - 118.64: 0 118.64 - 148.30: 1 Dihedral angle restraints: 1693 sinusoidal: 734 harmonic: 959 Sorted by residual: dihedral pdb=" C1 PC8 A 201 " pdb=" O3 PC8 A 201 " pdb=" P1 PC8 A 201 " pdb=" O4 PC8 A 201 " ideal model delta sinusoidal sigma weight residual 166.83 -44.87 -148.30 1 3.00e+01 1.11e-03 1.97e+01 dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 96 " pdb=" CB CYS C 96 " ideal model delta sinusoidal sigma weight residual -86.00 -118.46 32.46 1 1.00e+01 1.00e-02 1.50e+01 dihedral pdb=" CA GLU A 49 " pdb=" CB GLU A 49 " pdb=" CG GLU A 49 " pdb=" CD GLU A 49 " ideal model delta sinusoidal sigma weight residual 60.00 118.30 -58.30 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 1690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 282 0.042 - 0.083: 83 0.083 - 0.124: 20 0.124 - 0.165: 6 0.165 - 0.207: 1 Chirality restraints: 392 Sorted by residual: chirality pdb=" C7 PC8 A 201 " pdb=" C6 PC8 A 201 " pdb=" C8 PC8 A 201 " pdb=" O7 PC8 A 201 " both_signs ideal model delta sigma weight residual False -2.32 -2.53 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA PHE A 66 " pdb=" N PHE A 66 " pdb=" C PHE A 66 " pdb=" CB PHE A 66 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CA GLU B 21 " pdb=" N GLU B 21 " pdb=" C GLU B 21 " pdb=" CB GLU B 21 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.73e-01 ... (remaining 389 not shown) Planarity restraints: 464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 34 " -0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO B 35 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 35 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 35 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 66 " -0.015 2.00e-02 2.50e+03 1.31e-02 3.00e+00 pdb=" CG PHE A 66 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE A 66 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 66 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 66 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE A 66 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 66 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 29 " 0.026 5.00e-02 4.00e+02 3.86e-02 2.39e+00 pdb=" N PRO A 30 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 30 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 30 " 0.022 5.00e-02 4.00e+02 ... (remaining 461 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 852 2.82 - 3.34: 2563 3.34 - 3.86: 4571 3.86 - 4.38: 5225 4.38 - 4.90: 8698 Nonbonded interactions: 21909 Sorted by model distance: nonbonded pdb=" NH1 ARG C 38 " pdb=" OD1 ASP C 90 " model vdw 2.299 3.120 nonbonded pdb=" NE2 GLN C 13 " pdb=" O SER C 114 " model vdw 2.326 3.120 nonbonded pdb=" NE1 TRP B 82 " pdb=" O GLY A 29 " model vdw 2.337 3.120 nonbonded pdb=" OD1 ASP C 52 " pdb=" N SER C 57 " model vdw 2.339 3.120 nonbonded pdb=" N ASP A 17 " pdb=" OD1 ASP A 17 " model vdw 2.354 3.120 ... (remaining 21904 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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.150 Find NCS groups from input model: 0.030 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 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 : 0.009 0.106 2815 Z= 0.524 Angle : 0.932 15.635 3789 Z= 0.523 Chirality : 0.044 0.207 392 Planarity : 0.005 0.045 464 Dihedral : 19.172 148.303 1076 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.48 % Allowed : 17.41 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -1.35 (0.42), residues: 327 helix: -0.39 (0.35), residues: 169 sheet: -1.23 (0.64), residues: 57 loop : -1.25 (0.60), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 28 HIS 0.005 0.001 HIS A 84 PHE 0.027 0.002 PHE A 66 TYR 0.018 0.002 TYR C 95 ARG 0.002 0.000 ARG B 29 Details of bonding type rmsd hydrogen bonds : bond 0.11730 ( 166) hydrogen bonds : angle 5.43762 ( 465) SS BOND : bond 0.00508 ( 1) SS BOND : angle 1.10010 ( 2) covalent geometry : bond 0.00908 ( 2814) covalent geometry : angle 0.93148 ( 3787) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 GLN cc_start: 0.8003 (mm-40) cc_final: 0.7769 (tt0) REVERT: A 18 PHE cc_start: 0.6364 (t80) cc_final: 0.6059 (p90) outliers start: 4 outliers final: 4 residues processed: 87 average time/residue: 0.2066 time to fit residues: 20.3319 Evaluate side-chains 76 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 27 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 25 optimal weight: 0.0050 chunk 9 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.192002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.156736 restraints weight = 3838.713| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 2.83 r_work: 0.3745 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2815 Z= 0.131 Angle : 0.553 7.670 3789 Z= 0.284 Chirality : 0.040 0.131 392 Planarity : 0.005 0.053 464 Dihedral : 16.431 114.265 483 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.96 % Allowed : 23.33 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.69 (0.46), residues: 327 helix: 1.43 (0.38), residues: 178 sheet: -0.74 (0.74), residues: 49 loop : -0.54 (0.63), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 36 HIS 0.004 0.001 HIS A 84 PHE 0.013 0.001 PHE A 69 TYR 0.010 0.001 TYR C 95 ARG 0.009 0.001 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.03650 ( 166) hydrogen bonds : angle 4.43344 ( 465) SS BOND : bond 0.00277 ( 1) SS BOND : angle 0.95335 ( 2) covalent geometry : bond 0.00296 ( 2814) covalent geometry : angle 0.55299 ( 3787) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7606 (tt0) REVERT: C 43 LYS cc_start: 0.6523 (ttpt) cc_final: 0.6282 (ttpt) REVERT: C 102 TRP cc_start: 0.6132 (t-100) cc_final: 0.5784 (m-90) outliers start: 8 outliers final: 7 residues processed: 79 average time/residue: 0.1984 time to fit residues: 17.8814 Evaluate side-chains 78 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN C 54 GLN C 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.192865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.157754 restraints weight = 3781.856| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.84 r_work: 0.3764 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2815 Z= 0.132 Angle : 0.513 5.764 3789 Z= 0.265 Chirality : 0.040 0.135 392 Planarity : 0.005 0.064 464 Dihedral : 14.524 77.381 477 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.81 % Allowed : 24.44 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.25 (0.48), residues: 327 helix: 1.95 (0.39), residues: 180 sheet: -1.34 (0.69), residues: 50 loop : 0.05 (0.66), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 36 HIS 0.004 0.001 HIS A 84 PHE 0.013 0.001 PHE A 69 TYR 0.011 0.001 TYR C 95 ARG 0.004 0.001 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.03370 ( 166) hydrogen bonds : angle 4.33909 ( 465) SS BOND : bond 0.00741 ( 1) SS BOND : angle 0.21861 ( 2) covalent geometry : bond 0.00292 ( 2814) covalent geometry : angle 0.51314 ( 3787) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.293 Fit side-chains REVERT: B 26 GLU cc_start: 0.6883 (mp0) cc_final: 0.6565 (mp0) REVERT: B 119 GLN cc_start: 0.8038 (mm-40) cc_final: 0.7599 (tt0) REVERT: A 19 ARG cc_start: 0.7830 (ptt-90) cc_final: 0.6899 (ptt-90) REVERT: C 4 LEU cc_start: 0.7726 (mp) cc_final: 0.7512 (tp) REVERT: C 96 CYS cc_start: 0.5185 (OUTLIER) cc_final: 0.3876 (m) outliers start: 13 outliers final: 10 residues processed: 78 average time/residue: 0.1924 time to fit residues: 17.2297 Evaluate side-chains 79 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 31 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 GLN C 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.192590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.157610 restraints weight = 3822.231| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.83 r_work: 0.3731 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2815 Z= 0.164 Angle : 0.545 6.858 3789 Z= 0.279 Chirality : 0.041 0.128 392 Planarity : 0.005 0.063 464 Dihedral : 14.044 66.800 477 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 5.19 % Allowed : 25.93 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.47 (0.48), residues: 327 helix: 1.97 (0.39), residues: 180 sheet: -0.86 (0.68), residues: 56 loop : 0.36 (0.70), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 36 HIS 0.005 0.001 HIS A 84 PHE 0.018 0.002 PHE A 69 TYR 0.013 0.002 TYR C 95 ARG 0.004 0.001 ARG B 29 Details of bonding type rmsd hydrogen bonds : bond 0.03526 ( 166) hydrogen bonds : angle 4.31878 ( 465) SS BOND : bond 0.00730 ( 1) SS BOND : angle 0.16012 ( 2) covalent geometry : bond 0.00377 ( 2814) covalent geometry : angle 0.54466 ( 3787) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.262 Fit side-chains REVERT: B 119 GLN cc_start: 0.8003 (mm-40) cc_final: 0.7601 (tt0) REVERT: C 4 LEU cc_start: 0.7730 (mp) cc_final: 0.7513 (tp) REVERT: C 43 LYS cc_start: 0.6462 (ttpt) cc_final: 0.6236 (ttpt) REVERT: C 96 CYS cc_start: 0.5429 (OUTLIER) cc_final: 0.4241 (m) outliers start: 14 outliers final: 10 residues processed: 81 average time/residue: 0.1858 time to fit residues: 17.3450 Evaluate side-chains 82 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.193152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.158314 restraints weight = 3863.788| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.86 r_work: 0.3767 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2815 Z= 0.123 Angle : 0.503 7.703 3789 Z= 0.258 Chirality : 0.040 0.125 392 Planarity : 0.005 0.062 464 Dihedral : 13.482 64.286 477 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 5.93 % Allowed : 24.07 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.76 (0.49), residues: 327 helix: 2.12 (0.39), residues: 180 sheet: -0.61 (0.71), residues: 56 loop : 0.57 (0.71), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 36 HIS 0.004 0.001 HIS A 84 PHE 0.014 0.001 PHE A 69 TYR 0.012 0.001 TYR C 95 ARG 0.009 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03305 ( 166) hydrogen bonds : angle 4.14974 ( 465) SS BOND : bond 0.00804 ( 1) SS BOND : angle 0.47719 ( 2) covalent geometry : bond 0.00281 ( 2814) covalent geometry : angle 0.50280 ( 3787) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: B 119 GLN cc_start: 0.8014 (mm-40) cc_final: 0.7613 (tt0) REVERT: C 43 LYS cc_start: 0.6471 (ttpt) cc_final: 0.6251 (ttpt) REVERT: C 96 CYS cc_start: 0.5190 (OUTLIER) cc_final: 0.4282 (m) outliers start: 16 outliers final: 13 residues processed: 76 average time/residue: 0.2014 time to fit residues: 17.4151 Evaluate side-chains 79 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 9 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 0.0060 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 28 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 GLN C 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.193489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.159357 restraints weight = 3860.606| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.86 r_work: 0.3775 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2815 Z= 0.113 Angle : 0.508 5.766 3789 Z= 0.258 Chirality : 0.039 0.123 392 Planarity : 0.005 0.058 464 Dihedral : 12.924 62.035 477 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 5.19 % Allowed : 25.56 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.83 (0.49), residues: 327 helix: 2.19 (0.39), residues: 180 sheet: -0.76 (0.70), residues: 56 loop : 0.75 (0.71), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 36 HIS 0.004 0.001 HIS A 84 PHE 0.010 0.001 PHE A 69 TYR 0.010 0.001 TYR C 95 ARG 0.007 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03183 ( 166) hydrogen bonds : angle 4.12989 ( 465) SS BOND : bond 0.00477 ( 1) SS BOND : angle 0.69234 ( 2) covalent geometry : bond 0.00256 ( 2814) covalent geometry : angle 0.50806 ( 3787) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: B 15 ARG cc_start: 0.7215 (ttp80) cc_final: 0.6998 (ttp80) REVERT: B 119 GLN cc_start: 0.8039 (mm-40) cc_final: 0.7609 (tt0) REVERT: C 96 CYS cc_start: 0.5099 (OUTLIER) cc_final: 0.4883 (m) outliers start: 14 outliers final: 11 residues processed: 72 average time/residue: 0.1996 time to fit residues: 16.3420 Evaluate side-chains 74 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 23 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 13 optimal weight: 0.0060 chunk 5 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 1 optimal weight: 0.0470 chunk 30 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 9 optimal weight: 0.0170 chunk 18 optimal weight: 3.9990 overall best weight: 0.3132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 GLN C 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.196524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.162329 restraints weight = 3939.340| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 2.93 r_work: 0.3807 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2815 Z= 0.105 Angle : 0.532 8.235 3789 Z= 0.270 Chirality : 0.039 0.124 392 Planarity : 0.004 0.056 464 Dihedral : 12.591 61.233 477 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 3.70 % Allowed : 27.04 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.80 (0.48), residues: 327 helix: 2.18 (0.39), residues: 180 sheet: -1.25 (0.77), residues: 43 loop : 0.71 (0.67), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 36 HIS 0.003 0.001 HIS A 84 PHE 0.005 0.001 PHE A 66 TYR 0.009 0.001 TYR C 95 ARG 0.008 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03235 ( 166) hydrogen bonds : angle 4.08310 ( 465) SS BOND : bond 0.00377 ( 1) SS BOND : angle 0.36239 ( 2) covalent geometry : bond 0.00230 ( 2814) covalent geometry : angle 0.53194 ( 3787) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.287 Fit side-chains REVERT: B 15 ARG cc_start: 0.7153 (ttp80) cc_final: 0.6868 (ptt90) REVERT: B 119 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7624 (tt0) outliers start: 10 outliers final: 7 residues processed: 70 average time/residue: 0.2337 time to fit residues: 18.3318 Evaluate side-chains 70 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 54 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 16 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 22 optimal weight: 30.0000 chunk 12 optimal weight: 0.0670 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** 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 = 0.4247 r_free = 0.4247 target = 0.194978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.161210 restraints weight = 3828.311| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.87 r_work: 0.3789 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2815 Z= 0.126 Angle : 0.544 7.941 3789 Z= 0.276 Chirality : 0.040 0.122 392 Planarity : 0.005 0.056 464 Dihedral : 12.377 60.221 476 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.33 % Allowed : 25.56 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.76 (0.48), residues: 327 helix: 2.08 (0.38), residues: 180 sheet: -1.20 (0.66), residues: 56 loop : 1.15 (0.74), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 28 HIS 0.005 0.001 HIS A 84 PHE 0.012 0.001 PHE A 69 TYR 0.012 0.001 TYR C 80 ARG 0.008 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03381 ( 166) hydrogen bonds : angle 4.12292 ( 465) SS BOND : bond 0.00329 ( 1) SS BOND : angle 1.34858 ( 2) covalent geometry : bond 0.00288 ( 2814) covalent geometry : angle 0.54372 ( 3787) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.268 Fit side-chains REVERT: B 119 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7645 (tt0) outliers start: 9 outliers final: 7 residues processed: 66 average time/residue: 0.2229 time to fit residues: 16.6836 Evaluate side-chains 66 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 22 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 8 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 27 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 ASN ** A 33 ASN ** 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 = 0.4235 r_free = 0.4235 target = 0.193819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.159932 restraints weight = 3835.475| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.89 r_work: 0.3781 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2815 Z= 0.126 Angle : 0.542 7.742 3789 Z= 0.275 Chirality : 0.040 0.124 392 Planarity : 0.005 0.055 464 Dihedral : 12.333 59.354 476 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 4.44 % Allowed : 24.81 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.70 (0.49), residues: 327 helix: 2.08 (0.38), residues: 180 sheet: -1.32 (0.66), residues: 56 loop : 1.08 (0.75), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 28 HIS 0.005 0.001 HIS A 84 PHE 0.013 0.001 PHE A 69 TYR 0.010 0.001 TYR A 62 ARG 0.004 0.000 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03394 ( 166) hydrogen bonds : angle 4.08107 ( 465) SS BOND : bond 0.00170 ( 1) SS BOND : angle 1.60750 ( 2) covalent geometry : bond 0.00287 ( 2814) covalent geometry : angle 0.54058 ( 3787) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.296 Fit side-chains REVERT: B 119 GLN cc_start: 0.8038 (mm-40) cc_final: 0.7639 (tt0) REVERT: A 19 ARG cc_start: 0.7939 (ptt-90) cc_final: 0.6836 (ptt-90) outliers start: 12 outliers final: 11 residues processed: 69 average time/residue: 0.2142 time to fit residues: 16.8649 Evaluate side-chains 72 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 22 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.192933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.158987 restraints weight = 3901.792| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.87 r_work: 0.3775 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2815 Z= 0.136 Angle : 0.555 7.704 3789 Z= 0.282 Chirality : 0.041 0.124 392 Planarity : 0.005 0.055 464 Dihedral : 12.369 59.730 476 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 4.07 % Allowed : 24.81 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.69 (0.49), residues: 327 helix: 2.07 (0.38), residues: 180 sheet: -1.34 (0.65), residues: 56 loop : 1.08 (0.76), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 94 HIS 0.005 0.001 HIS A 84 PHE 0.014 0.001 PHE A 69 TYR 0.011 0.001 TYR A 62 ARG 0.007 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03402 ( 166) hydrogen bonds : angle 4.09663 ( 465) SS BOND : bond 0.00245 ( 1) SS BOND : angle 1.57573 ( 2) covalent geometry : bond 0.00314 ( 2814) covalent geometry : angle 0.55354 ( 3787) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.304 Fit side-chains REVERT: B 119 GLN cc_start: 0.8026 (mm-40) cc_final: 0.7626 (tt0) outliers start: 11 outliers final: 10 residues processed: 66 average time/residue: 0.2011 time to fit residues: 15.1125 Evaluate side-chains 70 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 54 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 28 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 2 optimal weight: 0.1980 chunk 29 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.201002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.162984 restraints weight = 4083.520| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 3.21 r_work: 0.3839 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2815 Z= 0.121 Angle : 0.545 7.577 3789 Z= 0.278 Chirality : 0.041 0.125 392 Planarity : 0.005 0.055 464 Dihedral : 12.286 59.610 476 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 4.81 % Allowed : 24.44 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.70 (0.49), residues: 327 helix: 2.10 (0.38), residues: 180 sheet: -1.37 (0.65), residues: 56 loop : 1.06 (0.76), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 28 HIS 0.005 0.001 HIS A 84 PHE 0.012 0.001 PHE A 69 TYR 0.010 0.001 TYR A 62 ARG 0.006 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03392 ( 166) hydrogen bonds : angle 4.07805 ( 465) SS BOND : bond 0.00201 ( 1) SS BOND : angle 1.39821 ( 2) covalent geometry : bond 0.00277 ( 2814) covalent geometry : angle 0.54383 ( 3787) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2069.13 seconds wall clock time: 36 minutes 49.61 seconds (2209.61 seconds total)