Starting phenix.real_space_refine on Wed Jun 4 15:56:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w5d_37286/06_2025/8w5d_37286.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w5d_37286/06_2025/8w5d_37286.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w5d_37286/06_2025/8w5d_37286.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w5d_37286/06_2025/8w5d_37286.map" model { file = "/net/cci-nas-00/data/ceres_data/8w5d_37286/06_2025/8w5d_37286.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w5d_37286/06_2025/8w5d_37286.cif" } resolution = 4.3 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= 0.019 sd= 0.087 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: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 2152 2.51 5 N 594 2.21 5 O 675 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 3431 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 869 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "C" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 944 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 8, 'TRANS': 118} Chain breaks: 1 Chain: "L" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 674 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 6, 'TRANS': 83} Chain breaks: 2 Restraints were copied for chains: c Time building chain proxies: 2.72, per 1000 atoms: 0.79 Number of scatterers: 3431 At special positions: 0 Unit cell: (92.4, 79.2, 81.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 675 8.00 N 594 7.00 C 2152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 396.8 milliseconds 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 836 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 9 sheets defined 12.1% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'c' and resid 101 through 116 removed outlier: 3.820A pdb=" N ARG c 105 " --> pdb=" O THR c 101 " (cutoff:3.500A) Processing helix chain 'c' and resid 118 through 127 Processing helix chain 'C' and resid 101 through 116 removed outlier: 3.820A pdb=" N ARG C 105 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 127 Processing sheet with id=AA1, first strand: chain 'H' and resid 21 through 23 Processing sheet with id=AA2, first strand: chain 'H' and resid 54 through 55 removed outlier: 3.797A pdb=" N ILE H 54 " --> pdb=" O VAL H 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 104 through 106 removed outlier: 3.552A pdb=" N TYR H 105 " --> pdb=" O THR C 7 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'c' and resid 22 through 26 removed outlier: 4.995A pdb=" N SER c 34 " --> pdb=" O ARG c 24 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N SER C 34 " --> pdb=" O ARG C 24 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'c' and resid 72 through 74 removed outlier: 7.610A pdb=" N THR c 72 " --> pdb=" O THR c 85 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR c 85 " --> pdb=" O THR c 72 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 72 through 74 removed outlier: 7.610A pdb=" N THR C 72 " --> pdb=" O THR C 85 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR C 85 " --> pdb=" O THR C 72 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA8, first strand: chain 'L' and resid 52 through 53 removed outlier: 3.923A pdb=" N LYS L 52 " --> pdb=" O GLN L 44 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLN L 44 " --> pdb=" O LYS L 52 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN L 97 " --> pdb=" O ASN L 41 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLN L 96 " --> pdb=" O GLY L 106 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLY L 106 " --> pdb=" O GLN L 96 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 71 through 72 95 hydrogen bonds defined for protein. 231 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: 0.75 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: 1.21 - 1.33: 788 1.33 - 1.45: 730 1.45 - 1.57: 1964 1.57 - 1.69: 0 1.69 - 1.81: 12 Bond restraints: 3494 Sorted by residual: bond pdb=" CA SER L 3 " pdb=" C SER L 3 " ideal model delta sigma weight residual 1.522 1.480 0.042 1.24e-02 6.50e+03 1.14e+01 bond pdb=" CA ASP L 4 " pdb=" C ASP L 4 " ideal model delta sigma weight residual 1.522 1.481 0.041 1.24e-02 6.50e+03 1.07e+01 bond pdb=" CA ASP L 4 " pdb=" CB ASP L 4 " ideal model delta sigma weight residual 1.535 1.475 0.060 1.90e-02 2.77e+03 1.01e+01 bond pdb=" CB ASP L 4 " pdb=" CG ASP L 4 " ideal model delta sigma weight residual 1.516 1.449 0.067 2.50e-02 1.60e+03 7.17e+00 bond pdb=" C VAL L 101 " pdb=" N PRO L 102 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.91e+00 ... (remaining 3489 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 4602 3.02 - 6.05: 124 6.05 - 9.07: 17 9.07 - 12.10: 4 12.10 - 15.12: 1 Bond angle restraints: 4748 Sorted by residual: angle pdb=" CA LYS H 78 " pdb=" CB LYS H 78 " pdb=" CG LYS H 78 " ideal model delta sigma weight residual 114.10 123.26 -9.16 2.00e+00 2.50e-01 2.10e+01 angle pdb=" CA LEU H 48 " pdb=" CB LEU H 48 " pdb=" CG LEU H 48 " ideal model delta sigma weight residual 116.30 131.42 -15.12 3.50e+00 8.16e-02 1.87e+01 angle pdb=" C GLY c 12 " pdb=" N LYS c 13 " pdb=" CA LYS c 13 " ideal model delta sigma weight residual 121.54 129.71 -8.17 1.91e+00 2.74e-01 1.83e+01 angle pdb=" C GLY C 12 " pdb=" N LYS C 13 " pdb=" CA LYS C 13 " ideal model delta sigma weight residual 121.54 129.64 -8.10 1.91e+00 2.74e-01 1.80e+01 angle pdb=" N VAL L 6 " pdb=" CA VAL L 6 " pdb=" C VAL L 6 " ideal model delta sigma weight residual 108.42 114.30 -5.88 1.43e+00 4.89e-01 1.69e+01 ... (remaining 4743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.89: 1927 14.89 - 29.77: 131 29.77 - 44.66: 29 44.66 - 59.54: 3 59.54 - 74.43: 6 Dihedral angle restraints: 2096 sinusoidal: 798 harmonic: 1298 Sorted by residual: dihedral pdb=" CA ASP c 14 " pdb=" C ASP c 14 " pdb=" N GLY c 15 " pdb=" CA GLY c 15 " ideal model delta harmonic sigma weight residual 180.00 149.24 30.76 0 5.00e+00 4.00e-02 3.78e+01 dihedral pdb=" CA ASP C 14 " pdb=" C ASP C 14 " pdb=" N GLY C 15 " pdb=" CA GLY C 15 " ideal model delta harmonic sigma weight residual 180.00 149.26 30.74 0 5.00e+00 4.00e-02 3.78e+01 dihedral pdb=" CA GLU H 49 " pdb=" C GLU H 49 " pdb=" N TRP H 50 " pdb=" CA TRP H 50 " ideal model delta harmonic sigma weight residual -180.00 -150.08 -29.92 0 5.00e+00 4.00e-02 3.58e+01 ... (remaining 2093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 359 0.053 - 0.106: 125 0.106 - 0.158: 52 0.158 - 0.211: 4 0.211 - 0.264: 4 Chirality restraints: 544 Sorted by residual: chirality pdb=" CG LEU L 53 " pdb=" CB LEU L 53 " pdb=" CD1 LEU L 53 " pdb=" CD2 LEU L 53 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA ILE L 5 " pdb=" N ILE L 5 " pdb=" C ILE L 5 " pdb=" CB ILE L 5 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB ILE C 68 " pdb=" CA ILE C 68 " pdb=" CG1 ILE C 68 " pdb=" CG2 ILE C 68 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 541 not shown) Planarity restraints: 620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 39 " -0.025 2.00e-02 2.50e+03 1.61e-02 6.51e+00 pdb=" CG TRP H 39 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP H 39 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP H 39 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 39 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP H 39 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP H 39 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 39 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 39 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP H 39 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL L 65 " 0.040 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO L 66 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO L 66 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO L 66 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS L 83 " -0.039 5.00e-02 4.00e+02 5.84e-02 5.47e+00 pdb=" N PRO L 84 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO L 84 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO L 84 " -0.033 5.00e-02 4.00e+02 ... (remaining 617 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 20 2.49 - 3.09: 2354 3.09 - 3.69: 4888 3.69 - 4.30: 6389 4.30 - 4.90: 10673 Nonbonded interactions: 24324 Sorted by model distance: nonbonded pdb=" CG2 VAL L 6 " pdb=" O THR L 23 " model vdw 1.882 3.460 nonbonded pdb=" CG2 VAL L 6 " pdb=" CA ILE L 24 " model vdw 2.126 3.890 nonbonded pdb=" CG2 VAL L 6 " pdb=" CD1 ILE L 24 " model vdw 2.195 3.880 nonbonded pdb=" OG SER H 102 " pdb=" O ASN H 111 " model vdw 2.241 3.040 nonbonded pdb=" OG SER H 31 " pdb=" O ASN c 10 " model vdw 2.287 3.040 ... (remaining 24319 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 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'c' } 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 group one per residue 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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.860 Find NCS groups from input model: 0.070 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 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 0.067 3494 Z= 0.340 Angle : 1.175 15.119 4748 Z= 0.627 Chirality : 0.063 0.264 544 Planarity : 0.008 0.060 620 Dihedral : 11.775 74.426 1260 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.23 % Allowed : 18.31 % Favored : 81.46 % Rotamer: Outliers : 0.79 % Allowed : 7.14 % Favored : 92.06 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: -4.56 (0.32), residues: 437 helix: -2.57 (0.52), residues: 46 sheet: -2.12 (0.45), residues: 118 loop : -3.76 (0.29), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.007 TRP H 39 HIS 0.011 0.004 HIS H 38 PHE 0.032 0.004 PHE H 113 TYR 0.034 0.003 TYR H 112 ARG 0.008 0.001 ARG H 41 Details of bonding type rmsd hydrogen bonds : bond 0.16497 ( 95) hydrogen bonds : angle 7.36503 ( 231) covalent geometry : bond 0.00733 ( 3494) covalent geometry : angle 1.17477 ( 4748) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 154 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 42 GLN cc_start: 0.8897 (tm-30) cc_final: 0.8691 (tm-30) REVERT: H 48 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8653 (pp) REVERT: H 105 TYR cc_start: 0.8231 (m-10) cc_final: 0.7856 (m-10) REVERT: c 63 LYS cc_start: 0.8370 (mttt) cc_final: 0.8168 (mtpt) REVERT: C 2 LYS cc_start: 0.8728 (tptt) cc_final: 0.8207 (tptt) REVERT: C 24 ARG cc_start: 0.8229 (ttm-80) cc_final: 0.7902 (mmt180) REVERT: L 40 MET cc_start: 0.8598 (tpt) cc_final: 0.8290 (tpt) REVERT: L 55 ILE cc_start: 0.7972 (pp) cc_final: 0.7733 (pt) REVERT: L 80 LEU cc_start: 0.8590 (tp) cc_final: 0.8355 (tp) outliers start: 3 outliers final: 1 residues processed: 156 average time/residue: 0.2008 time to fit residues: 36.1025 Evaluate side-chains 92 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 90 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 11 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 40.0000 chunk 33 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN c 22 ASN ** c 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 69 GLN C 22 ASN ** L 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.069758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.059261 restraints weight = 14770.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.061017 restraints weight = 8499.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.062251 restraints weight = 5674.154| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 3494 Z= 0.230 Angle : 0.817 9.380 4748 Z= 0.426 Chirality : 0.047 0.166 544 Planarity : 0.007 0.074 620 Dihedral : 7.292 33.603 479 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.04 % Favored : 86.96 % Rotamer: Outliers : 0.26 % Allowed : 3.44 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: -4.25 (0.33), residues: 437 helix: -1.76 (0.64), residues: 48 sheet: -1.99 (0.41), residues: 135 loop : -3.70 (0.30), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP H 39 HIS 0.007 0.002 HIS H 38 PHE 0.029 0.003 PHE L 78 TYR 0.016 0.002 TYR L 103 ARG 0.013 0.001 ARG L 21 Details of bonding type rmsd hydrogen bonds : bond 0.04203 ( 95) hydrogen bonds : angle 5.97315 ( 231) covalent geometry : bond 0.00508 ( 3494) covalent geometry : angle 0.81747 ( 4748) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 114 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 19 GLN cc_start: 0.8864 (mt0) cc_final: 0.8476 (mt0) REVERT: H 42 GLN cc_start: 0.9189 (tm-30) cc_final: 0.8919 (tm-30) REVERT: H 73 ARG cc_start: 0.8767 (ttp-110) cc_final: 0.8526 (ttp-110) REVERT: H 75 ASP cc_start: 0.8976 (m-30) cc_final: 0.8772 (m-30) REVERT: H 105 TYR cc_start: 0.8950 (m-10) cc_final: 0.8393 (m-10) REVERT: c 13 LYS cc_start: 0.9411 (ttmm) cc_final: 0.9123 (ttmm) REVERT: c 37 GLN cc_start: 0.8731 (tm-30) cc_final: 0.8204 (tm-30) REVERT: c 69 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7432 (pp30) REVERT: c 95 SER cc_start: 0.8842 (t) cc_final: 0.8597 (p) REVERT: c 122 ILE cc_start: 0.8976 (pt) cc_final: 0.8625 (pt) REVERT: c 127 GLN cc_start: 0.8837 (mp10) cc_final: 0.8311 (mp10) REVERT: C 11 ILE cc_start: 0.9439 (pt) cc_final: 0.9112 (pt) REVERT: C 19 LEU cc_start: 0.8793 (tp) cc_final: 0.8591 (tp) REVERT: C 37 GLN cc_start: 0.8862 (tm-30) cc_final: 0.8600 (tm-30) REVERT: L 60 ASN cc_start: 0.8768 (m110) cc_final: 0.8152 (m110) REVERT: L 80 LEU cc_start: 0.8431 (tp) cc_final: 0.8228 (tt) outliers start: 1 outliers final: 0 residues processed: 115 average time/residue: 0.1634 time to fit residues: 22.5764 Evaluate side-chains 85 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 17 optimal weight: 40.0000 chunk 3 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 69 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 = 0.3089 r_free = 0.3089 target = 0.069070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.058899 restraints weight = 14466.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.060594 restraints weight = 8502.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.061729 restraints weight = 5699.493| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 3494 Z= 0.233 Angle : 0.791 9.956 4748 Z= 0.412 Chirality : 0.046 0.145 544 Planarity : 0.005 0.045 620 Dihedral : 6.976 37.403 479 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.87 % Favored : 85.13 % Rotamer: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: -3.91 (0.35), residues: 437 helix: -1.63 (0.66), residues: 48 sheet: -1.56 (0.47), residues: 126 loop : -3.51 (0.31), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP H 55 HIS 0.008 0.002 HIS H 38 PHE 0.026 0.002 PHE L 78 TYR 0.014 0.002 TYR H 105 ARG 0.004 0.001 ARG L 21 Details of bonding type rmsd hydrogen bonds : bond 0.04074 ( 95) hydrogen bonds : angle 5.80079 ( 231) covalent geometry : bond 0.00505 ( 3494) covalent geometry : angle 0.79121 ( 4748) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 19 GLN cc_start: 0.8764 (mt0) cc_final: 0.8475 (mt0) REVERT: H 73 ARG cc_start: 0.8873 (ttp-110) cc_final: 0.8204 (ttp-110) REVERT: H 75 ASP cc_start: 0.9051 (m-30) cc_final: 0.8819 (m-30) REVERT: H 105 TYR cc_start: 0.9179 (m-80) cc_final: 0.8476 (m-10) REVERT: c 37 GLN cc_start: 0.8732 (tm-30) cc_final: 0.8207 (tm-30) REVERT: c 65 GLN cc_start: 0.8412 (tm-30) cc_final: 0.8031 (tm-30) REVERT: c 67 LYS cc_start: 0.9055 (ttmm) cc_final: 0.8643 (ttmm) REVERT: c 122 ILE cc_start: 0.8973 (pt) cc_final: 0.8679 (pt) REVERT: c 127 GLN cc_start: 0.8973 (mp10) cc_final: 0.8324 (mp10) REVERT: C 11 ILE cc_start: 0.9438 (pt) cc_final: 0.8985 (pt) REVERT: C 111 GLU cc_start: 0.9119 (pt0) cc_final: 0.8816 (pt0) REVERT: L 27 ARG cc_start: 0.8489 (ptp-170) cc_final: 0.8232 (ptp-170) REVERT: L 80 LEU cc_start: 0.8436 (tp) cc_final: 0.8113 (tt) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1686 time to fit residues: 21.5997 Evaluate side-chains 79 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 9 optimal weight: 5.9990 chunk 35 optimal weight: 30.0000 chunk 28 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 3 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 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 = 0.3145 r_free = 0.3145 target = 0.071146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.060797 restraints weight = 14349.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.062594 restraints weight = 8249.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.063858 restraints weight = 5494.814| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3494 Z= 0.125 Angle : 0.734 8.738 4748 Z= 0.376 Chirality : 0.046 0.140 544 Planarity : 0.004 0.043 620 Dihedral : 6.510 36.707 479 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: -3.58 (0.37), residues: 437 helix: -1.32 (0.71), residues: 48 sheet: -1.41 (0.45), residues: 135 loop : -3.31 (0.33), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 110 HIS 0.002 0.001 HIS H 38 PHE 0.016 0.002 PHE L 78 TYR 0.010 0.001 TYR L 103 ARG 0.003 0.000 ARG c 105 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 95) hydrogen bonds : angle 5.50075 ( 231) covalent geometry : bond 0.00274 ( 3494) covalent geometry : angle 0.73398 ( 4748) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 19 GLN cc_start: 0.8565 (mt0) cc_final: 0.8297 (mt0) REVERT: H 42 GLN cc_start: 0.9110 (tm-30) cc_final: 0.8770 (tm-30) REVERT: H 50 TRP cc_start: 0.7879 (p-90) cc_final: 0.7556 (p-90) REVERT: H 71 SER cc_start: 0.9236 (m) cc_final: 0.8774 (p) REVERT: H 73 ARG cc_start: 0.8773 (ttp-110) cc_final: 0.8163 (ttp-110) REVERT: H 80 GLN cc_start: 0.9057 (mm110) cc_final: 0.8809 (mm-40) REVERT: H 84 LYS cc_start: 0.9127 (ttpp) cc_final: 0.8883 (tmtt) REVERT: H 101 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8236 (tm-30) REVERT: H 105 TYR cc_start: 0.9028 (m-80) cc_final: 0.8607 (m-10) REVERT: H 108 ASN cc_start: 0.9259 (m-40) cc_final: 0.8831 (t0) REVERT: c 37 GLN cc_start: 0.8737 (tm-30) cc_final: 0.7994 (tm-30) REVERT: c 65 GLN cc_start: 0.8382 (tm-30) cc_final: 0.8030 (tm-30) REVERT: c 67 LYS cc_start: 0.9100 (ttmm) cc_final: 0.8684 (ttmm) REVERT: c 102 ASP cc_start: 0.9249 (p0) cc_final: 0.8977 (p0) REVERT: c 122 ILE cc_start: 0.8923 (pt) cc_final: 0.8617 (pt) REVERT: c 127 GLN cc_start: 0.8915 (mp10) cc_final: 0.8340 (mp10) REVERT: C 11 ILE cc_start: 0.9377 (pt) cc_final: 0.9027 (pt) REVERT: C 69 GLN cc_start: 0.9031 (pt0) cc_final: 0.8785 (mt0) REVERT: C 111 GLU cc_start: 0.9180 (pt0) cc_final: 0.8844 (pt0) REVERT: L 49 GLN cc_start: 0.8341 (pm20) cc_final: 0.8136 (pm20) REVERT: L 80 LEU cc_start: 0.8247 (tp) cc_final: 0.7949 (tt) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1519 time to fit residues: 20.4206 Evaluate side-chains 88 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 31 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 17 optimal weight: 40.0000 chunk 14 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 15 optimal weight: 0.0570 chunk 24 optimal weight: 8.9990 chunk 8 optimal weight: 20.0000 chunk 41 optimal weight: 0.0970 chunk 32 optimal weight: 5.9990 overall best weight: 3.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 10 ASN ** c 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 GLN ** 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 = 0.3125 r_free = 0.3125 target = 0.070309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.060075 restraints weight = 14689.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.061817 restraints weight = 8298.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.063027 restraints weight = 5491.304| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3494 Z= 0.183 Angle : 0.759 9.374 4748 Z= 0.390 Chirality : 0.046 0.145 544 Planarity : 0.004 0.041 620 Dihedral : 6.496 36.235 479 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.87 % Favored : 85.13 % Rotamer: Outliers : 0.26 % Allowed : 2.65 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: -3.33 (0.38), residues: 437 helix: -1.44 (0.69), residues: 48 sheet: -1.32 (0.45), residues: 145 loop : -3.07 (0.35), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 55 HIS 0.001 0.001 HIS H 38 PHE 0.017 0.002 PHE L 78 TYR 0.018 0.001 TYR L 103 ARG 0.002 0.000 ARG H 69 Details of bonding type rmsd hydrogen bonds : bond 0.03533 ( 95) hydrogen bonds : angle 5.65652 ( 231) covalent geometry : bond 0.00397 ( 3494) covalent geometry : angle 0.75865 ( 4748) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 19 GLN cc_start: 0.8656 (mt0) cc_final: 0.8277 (mt0) REVERT: H 42 GLN cc_start: 0.9214 (tm-30) cc_final: 0.8935 (tm-30) REVERT: H 50 TRP cc_start: 0.8051 (p-90) cc_final: 0.7686 (p-90) REVERT: H 71 SER cc_start: 0.9356 (m) cc_final: 0.8768 (p) REVERT: H 75 ASP cc_start: 0.8924 (m-30) cc_final: 0.8704 (m-30) REVERT: H 80 GLN cc_start: 0.8848 (mm110) cc_final: 0.8362 (mm-40) REVERT: H 84 LYS cc_start: 0.9235 (ttpp) cc_final: 0.8773 (tmtt) REVERT: H 89 GLN cc_start: 0.8573 (tm-30) cc_final: 0.8198 (tm-30) REVERT: H 101 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8214 (tm-30) REVERT: H 105 TYR cc_start: 0.9115 (m-80) cc_final: 0.8673 (m-10) REVERT: c 37 GLN cc_start: 0.8711 (tm-30) cc_final: 0.8142 (tm-30) REVERT: c 46 LYS cc_start: 0.8486 (mmtm) cc_final: 0.8096 (mmmt) REVERT: c 65 GLN cc_start: 0.8374 (tm-30) cc_final: 0.8001 (tm-30) REVERT: c 67 LYS cc_start: 0.9095 (ttmm) cc_final: 0.8649 (ttmm) REVERT: C 11 ILE cc_start: 0.9312 (pt) cc_final: 0.9028 (pt) REVERT: C 37 GLN cc_start: 0.8924 (tm-30) cc_final: 0.8702 (tm-30) REVERT: C 46 LYS cc_start: 0.8824 (mptt) cc_final: 0.8243 (mtmt) REVERT: C 70 ASN cc_start: 0.9132 (m-40) cc_final: 0.8932 (m-40) REVERT: C 111 GLU cc_start: 0.9217 (pt0) cc_final: 0.8816 (pt0) outliers start: 1 outliers final: 0 residues processed: 104 average time/residue: 0.1573 time to fit residues: 19.7688 Evaluate side-chains 86 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 4 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 34 optimal weight: 20.0000 chunk 41 optimal weight: 0.9980 chunk 1 optimal weight: 0.0570 chunk 5 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 overall best weight: 2.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 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 = 0.3145 r_free = 0.3145 target = 0.071589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.060937 restraints weight = 14345.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.062823 restraints weight = 7876.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.064137 restraints weight = 5102.948| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3494 Z= 0.140 Angle : 0.754 9.959 4748 Z= 0.390 Chirality : 0.046 0.151 544 Planarity : 0.005 0.051 620 Dihedral : 6.374 36.256 479 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: -3.12 (0.39), residues: 437 helix: -1.35 (0.70), residues: 48 sheet: -1.16 (0.46), residues: 145 loop : -2.92 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 110 HIS 0.004 0.001 HIS L 83 PHE 0.012 0.001 PHE L 78 TYR 0.008 0.001 TYR L 103 ARG 0.007 0.001 ARG H 73 Details of bonding type rmsd hydrogen bonds : bond 0.03557 ( 95) hydrogen bonds : angle 5.46267 ( 231) covalent geometry : bond 0.00303 ( 3494) covalent geometry : angle 0.75375 ( 4748) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 19 GLN cc_start: 0.8635 (mt0) cc_final: 0.8222 (mt0) REVERT: H 32 LEU cc_start: 0.9239 (tp) cc_final: 0.8909 (tp) REVERT: H 35 TYR cc_start: 0.8443 (m-80) cc_final: 0.8207 (m-80) REVERT: H 42 GLN cc_start: 0.9172 (tm-30) cc_final: 0.8877 (tm-30) REVERT: H 50 TRP cc_start: 0.7812 (p-90) cc_final: 0.7564 (p-90) REVERT: H 54 ILE cc_start: 0.9002 (pt) cc_final: 0.7958 (mm) REVERT: H 71 SER cc_start: 0.9320 (m) cc_final: 0.8814 (p) REVERT: H 73 ARG cc_start: 0.8837 (ttp-110) cc_final: 0.8136 (ttp-110) REVERT: H 80 GLN cc_start: 0.8818 (mm110) cc_final: 0.8392 (mm-40) REVERT: H 101 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8041 (tm-30) REVERT: H 105 TYR cc_start: 0.8999 (m-80) cc_final: 0.8474 (m-10) REVERT: c 37 GLN cc_start: 0.8794 (tm-30) cc_final: 0.8095 (tm-30) REVERT: c 65 GLN cc_start: 0.8419 (tm-30) cc_final: 0.8043 (tm-30) REVERT: c 67 LYS cc_start: 0.9075 (ttmm) cc_final: 0.8667 (ttmm) REVERT: c 109 ARG cc_start: 0.9369 (ttp80) cc_final: 0.8842 (tmm-80) REVERT: C 37 GLN cc_start: 0.8952 (tm-30) cc_final: 0.8643 (tm-30) REVERT: C 46 LYS cc_start: 0.8895 (mptt) cc_final: 0.8430 (mtmt) REVERT: C 69 GLN cc_start: 0.8975 (mt0) cc_final: 0.8566 (mt0) REVERT: C 111 GLU cc_start: 0.9185 (pt0) cc_final: 0.8889 (pt0) REVERT: L 99 LYS cc_start: 0.8420 (mmmm) cc_final: 0.7993 (mmmm) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1620 time to fit residues: 20.0920 Evaluate side-chains 81 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 40 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 18 optimal weight: 20.0000 chunk 6 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 ASN ** c 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 ASN ** L 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.069572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.059246 restraints weight = 14389.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.061021 restraints weight = 8028.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.062229 restraints weight = 5272.891| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.5418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 3494 Z= 0.229 Angle : 0.820 10.016 4748 Z= 0.422 Chirality : 0.048 0.152 544 Planarity : 0.004 0.027 620 Dihedral : 6.647 38.168 479 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.56 % Favored : 84.44 % Rotamer: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -3.25 (0.38), residues: 437 helix: -1.50 (0.67), residues: 48 sheet: -1.37 (0.46), residues: 139 loop : -2.88 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 55 HIS 0.011 0.003 HIS L 83 PHE 0.022 0.002 PHE H 113 TYR 0.014 0.002 TYR H 112 ARG 0.006 0.001 ARG L 21 Details of bonding type rmsd hydrogen bonds : bond 0.03617 ( 95) hydrogen bonds : angle 5.49825 ( 231) covalent geometry : bond 0.00497 ( 3494) covalent geometry : angle 0.82025 ( 4748) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 19 GLN cc_start: 0.8780 (mt0) cc_final: 0.8301 (mt0) REVERT: H 35 TYR cc_start: 0.8545 (m-80) cc_final: 0.8128 (m-80) REVERT: H 71 SER cc_start: 0.9394 (m) cc_final: 0.8747 (p) REVERT: H 75 ASP cc_start: 0.9067 (m-30) cc_final: 0.8862 (m-30) REVERT: H 80 GLN cc_start: 0.8923 (mm110) cc_final: 0.8515 (mm-40) REVERT: H 101 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8189 (tm-30) REVERT: H 105 TYR cc_start: 0.9007 (m-80) cc_final: 0.8545 (m-10) REVERT: c 65 GLN cc_start: 0.8483 (tm-30) cc_final: 0.8086 (tm-30) REVERT: c 67 LYS cc_start: 0.9057 (ttmm) cc_final: 0.8602 (ttmm) REVERT: C 46 LYS cc_start: 0.9130 (mptt) cc_final: 0.8803 (mttm) REVERT: C 47 ARG cc_start: 0.9147 (mtm110) cc_final: 0.8765 (mtp85) REVERT: C 69 GLN cc_start: 0.8959 (mt0) cc_final: 0.8379 (mt0) REVERT: C 70 ASN cc_start: 0.9119 (m-40) cc_final: 0.8723 (m-40) REVERT: C 111 GLU cc_start: 0.9188 (pt0) cc_final: 0.8791 (pt0) REVERT: L 40 MET cc_start: 0.9317 (tpt) cc_final: 0.8906 (tpt) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1545 time to fit residues: 17.0054 Evaluate side-chains 70 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 40 optimal weight: 20.0000 chunk 33 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 16 GLN ** H 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 GLN ** 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 = 0.3094 r_free = 0.3094 target = 0.068859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.058676 restraints weight = 14513.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.060487 restraints weight = 7952.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.061727 restraints weight = 5138.593| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.5654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 3494 Z= 0.224 Angle : 0.825 9.679 4748 Z= 0.423 Chirality : 0.047 0.145 544 Planarity : 0.005 0.053 620 Dihedral : 6.775 37.450 479 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.19 % Favored : 85.81 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: -3.18 (0.39), residues: 437 helix: -1.34 (0.69), residues: 48 sheet: -1.54 (0.43), residues: 152 loop : -2.74 (0.38), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP H 50 HIS 0.004 0.002 HIS L 83 PHE 0.026 0.002 PHE H 113 TYR 0.031 0.002 TYR H 112 ARG 0.009 0.001 ARG H 73 Details of bonding type rmsd hydrogen bonds : bond 0.03611 ( 95) hydrogen bonds : angle 5.58567 ( 231) covalent geometry : bond 0.00493 ( 3494) covalent geometry : angle 0.82526 ( 4748) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 19 GLN cc_start: 0.8758 (mt0) cc_final: 0.8303 (mt0) REVERT: H 35 TYR cc_start: 0.8613 (m-80) cc_final: 0.8158 (m-80) REVERT: H 71 SER cc_start: 0.9412 (m) cc_final: 0.8799 (p) REVERT: H 80 GLN cc_start: 0.8999 (mm110) cc_final: 0.8557 (mm-40) REVERT: H 101 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8150 (tm-30) REVERT: H 105 TYR cc_start: 0.9028 (m-80) cc_final: 0.8489 (m-10) REVERT: c 65 GLN cc_start: 0.8473 (tm-30) cc_final: 0.8025 (tm-30) REVERT: c 67 LYS cc_start: 0.9063 (ttmm) cc_final: 0.8605 (ttmm) REVERT: C 46 LYS cc_start: 0.9007 (mptt) cc_final: 0.8543 (mttt) REVERT: C 69 GLN cc_start: 0.8960 (mt0) cc_final: 0.8498 (mt0) REVERT: C 70 ASN cc_start: 0.9132 (m-40) cc_final: 0.8782 (m-40) REVERT: C 111 GLU cc_start: 0.9202 (pt0) cc_final: 0.8793 (pt0) REVERT: C 121 LEU cc_start: 0.9592 (mm) cc_final: 0.9333 (mt) REVERT: L 99 LYS cc_start: 0.8597 (tptm) cc_final: 0.8275 (mmmt) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1523 time to fit residues: 17.2525 Evaluate side-chains 72 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 17 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 2 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 ASN ** c 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 ASN ** L 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.071871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.061638 restraints weight = 14169.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.063489 restraints weight = 7808.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.064739 restraints weight = 5078.003| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.5734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3494 Z= 0.142 Angle : 0.781 8.963 4748 Z= 0.396 Chirality : 0.047 0.140 544 Planarity : 0.004 0.020 620 Dihedral : 6.330 35.509 479 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.04 % Favored : 86.96 % Rotamer: Outliers : 0.26 % Allowed : 0.26 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.87 (0.40), residues: 437 helix: -1.15 (0.72), residues: 48 sheet: -1.07 (0.45), residues: 149 loop : -2.71 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 110 HIS 0.004 0.001 HIS L 83 PHE 0.020 0.002 PHE H 113 TYR 0.016 0.001 TYR H 112 ARG 0.006 0.001 ARG C 47 Details of bonding type rmsd hydrogen bonds : bond 0.03372 ( 95) hydrogen bonds : angle 5.43218 ( 231) covalent geometry : bond 0.00314 ( 3494) covalent geometry : angle 0.78101 ( 4748) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 35 TYR cc_start: 0.8718 (m-80) cc_final: 0.8377 (m-80) REVERT: H 42 GLN cc_start: 0.9255 (tm-30) cc_final: 0.8966 (tm-30) REVERT: H 54 ILE cc_start: 0.8906 (pt) cc_final: 0.8104 (mm) REVERT: H 71 SER cc_start: 0.9411 (m) cc_final: 0.8785 (p) REVERT: H 80 GLN cc_start: 0.9071 (mm110) cc_final: 0.8697 (mm-40) REVERT: H 101 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7941 (tm-30) REVERT: H 105 TYR cc_start: 0.8935 (m-80) cc_final: 0.8462 (m-10) REVERT: c 14 ASP cc_start: 0.8543 (p0) cc_final: 0.8238 (p0) REVERT: c 65 GLN cc_start: 0.8473 (tm-30) cc_final: 0.8084 (tm-30) REVERT: c 67 LYS cc_start: 0.9083 (ttmm) cc_final: 0.8624 (ttmm) REVERT: C 46 LYS cc_start: 0.9225 (mptt) cc_final: 0.8901 (mttm) REVERT: C 47 ARG cc_start: 0.9219 (mtm-85) cc_final: 0.8399 (ttm-80) REVERT: C 69 GLN cc_start: 0.8897 (mt0) cc_final: 0.8455 (mt0) REVERT: C 70 ASN cc_start: 0.9115 (m-40) cc_final: 0.8750 (m-40) REVERT: C 111 GLU cc_start: 0.9190 (pt0) cc_final: 0.8754 (pt0) REVERT: C 121 LEU cc_start: 0.9553 (mm) cc_final: 0.9293 (mt) outliers start: 1 outliers final: 0 residues processed: 103 average time/residue: 0.1599 time to fit residues: 20.1259 Evaluate side-chains 81 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 16 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 29 optimal weight: 0.0870 chunk 18 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 34 optimal weight: 20.0000 overall best weight: 3.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 ASN L 81 ASN L 97 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.071591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.061356 restraints weight = 14638.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.063110 restraints weight = 8356.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.064354 restraints weight = 5533.992| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.5999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3494 Z= 0.167 Angle : 0.807 9.340 4748 Z= 0.412 Chirality : 0.047 0.140 544 Planarity : 0.004 0.038 620 Dihedral : 6.282 32.705 479 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.27 % Favored : 86.73 % Rotamer: Outliers : 0.53 % Allowed : 0.26 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.94 (0.39), residues: 437 helix: -1.14 (0.71), residues: 48 sheet: -1.34 (0.43), residues: 152 loop : -2.60 (0.38), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP H 50 HIS 0.003 0.001 HIS L 83 PHE 0.021 0.002 PHE H 113 TYR 0.016 0.002 TYR L 103 ARG 0.009 0.001 ARG H 73 Details of bonding type rmsd hydrogen bonds : bond 0.03485 ( 95) hydrogen bonds : angle 5.39085 ( 231) covalent geometry : bond 0.00375 ( 3494) covalent geometry : angle 0.80651 ( 4748) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 35 TYR cc_start: 0.8718 (m-80) cc_final: 0.8393 (m-80) REVERT: H 42 GLN cc_start: 0.9243 (tm-30) cc_final: 0.8984 (tm-30) REVERT: H 71 SER cc_start: 0.9422 (m) cc_final: 0.8823 (p) REVERT: H 78 LYS cc_start: 0.9007 (pttm) cc_final: 0.8631 (pttp) REVERT: H 80 GLN cc_start: 0.8879 (mm110) cc_final: 0.8407 (mm-40) REVERT: H 101 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8115 (tm-30) REVERT: H 105 TYR cc_start: 0.8375 (m-80) cc_final: 0.8026 (m-10) REVERT: c 14 ASP cc_start: 0.8481 (p0) cc_final: 0.8197 (p0) REVERT: c 65 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8243 (tm-30) REVERT: C 46 LYS cc_start: 0.9249 (mptt) cc_final: 0.8933 (mttm) REVERT: C 47 ARG cc_start: 0.9129 (mtm-85) cc_final: 0.8415 (ttm-80) REVERT: C 69 GLN cc_start: 0.8882 (mt0) cc_final: 0.8642 (mt0) REVERT: C 70 ASN cc_start: 0.9074 (m-40) cc_final: 0.8682 (m-40) REVERT: C 111 GLU cc_start: 0.9157 (pt0) cc_final: 0.8730 (pt0) REVERT: C 115 LEU cc_start: 0.9752 (tp) cc_final: 0.9515 (tt) REVERT: C 121 LEU cc_start: 0.9568 (mm) cc_final: 0.9129 (mm) outliers start: 2 outliers final: 0 residues processed: 100 average time/residue: 0.2038 time to fit residues: 24.2978 Evaluate side-chains 81 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 41 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 ASN ** L 97 GLN ** 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 = 0.3096 r_free = 0.3096 target = 0.069949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.059639 restraints weight = 14946.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.061413 restraints weight = 8261.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.062654 restraints weight = 5409.952| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.6089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 3494 Z= 0.227 Angle : 0.854 9.917 4748 Z= 0.435 Chirality : 0.047 0.144 544 Planarity : 0.005 0.037 620 Dihedral : 6.462 34.001 479 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.79 % Favored : 84.21 % Rotamer: Outliers : 0.26 % Allowed : 0.26 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -3.05 (0.38), residues: 437 helix: -1.23 (0.70), residues: 48 sheet: -1.50 (0.42), residues: 152 loop : -2.61 (0.38), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP H 55 HIS 0.005 0.002 HIS L 83 PHE 0.014 0.002 PHE L 78 TYR 0.019 0.002 TYR H 112 ARG 0.009 0.001 ARG H 73 Details of bonding type rmsd hydrogen bonds : bond 0.03666 ( 95) hydrogen bonds : angle 5.50692 ( 231) covalent geometry : bond 0.00495 ( 3494) covalent geometry : angle 0.85378 ( 4748) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1408.90 seconds wall clock time: 25 minutes 20.19 seconds (1520.19 seconds total)