Starting phenix.real_space_refine on Fri Dec 27 11:25:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sj0_25149/12_2024/7sj0_25149.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sj0_25149/12_2024/7sj0_25149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sj0_25149/12_2024/7sj0_25149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sj0_25149/12_2024/7sj0_25149.map" model { file = "/net/cci-nas-00/data/ceres_data/7sj0_25149/12_2024/7sj0_25149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sj0_25149/12_2024/7sj0_25149.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 812 atoms to isotropic. 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 14 5.16 5 C 2279 2.51 5 N 593 2.21 5 O 704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3590 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1806 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 10, 'TRANS': 213} Chain breaks: 4 Chain: "B" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 930 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 114} Chain: "L" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 784 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 4.02, per 1000 atoms: 1.12 Number of scatterers: 3590 At special positions: 0 Unit cell: (99, 78.1, 94.6, 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 14 16.00 O 704 8.00 N 593 7.00 C 2279 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 17 " " NAG A1304 " - " ASN A 61 " " NAG A1305 " - " ASN A 149 " Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 416.8 milliseconds 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 824 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 9 sheets defined 2.0% alpha, 36.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 156 through 159 Processing helix chain 'B' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 29 removed outlier: 4.312A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TRP A 64 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 79 removed outlier: 4.045A pdb=" N ARG A 78 " --> pdb=" O HIS A 69 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N HIS A 69 " --> pdb=" O ARG A 78 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.702A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 151 through 155 removed outlier: 4.000A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.735A pdb=" N GLN B 3 " --> pdb=" O SER B 25 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 11 removed outlier: 3.846A pdb=" N THR B 119 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 118 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA B 92 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY B 99 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER B 33 " --> pdb=" O GLY B 99 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N MET B 34 " --> pdb=" O GLY B 50 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLY B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA B 40 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 11 through 12 Processing sheet with id=AA8, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.525A pdb=" N VAL L 18 " --> pdb=" O ILE L 76 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE L 76 " --> pdb=" O VAL L 18 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 46 through 50 removed outlier: 3.640A pdb=" N GLN L 38 " --> pdb=" O LYS L 46 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER L 35 " --> pdb=" O GLY L 90 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY L 90 " --> pdb=" O SER L 35 " (cutoff:3.500A) 93 hydrogen bonds defined for protein. 228 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: 0.92 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1130 1.34 - 1.46: 942 1.46 - 1.58: 1584 1.58 - 1.70: 0 1.70 - 1.82: 20 Bond restraints: 3676 Sorted by residual: bond pdb=" C1 NAG A1305 " pdb=" O5 NAG A1305 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.14e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.96e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.94e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.76e+00 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.56e+00 ... (remaining 3671 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 4795 1.51 - 3.02: 173 3.02 - 4.53: 22 4.53 - 6.04: 4 6.04 - 7.54: 2 Bond angle restraints: 4996 Sorted by residual: angle pdb=" CA THR A 33 " pdb=" CB THR A 33 " pdb=" CG2 THR A 33 " ideal model delta sigma weight residual 110.50 114.45 -3.95 1.70e+00 3.46e-01 5.39e+00 angle pdb=" CA CYS A 131 " pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " ideal model delta sigma weight residual 114.40 119.53 -5.13 2.30e+00 1.89e-01 4.98e+00 angle pdb=" CA LEU L 96 " pdb=" CB LEU L 96 " pdb=" CG LEU L 96 " ideal model delta sigma weight residual 116.30 123.84 -7.54 3.50e+00 8.16e-02 4.65e+00 angle pdb=" CB MET B 34 " pdb=" CG MET B 34 " pdb=" SD MET B 34 " ideal model delta sigma weight residual 112.70 118.84 -6.14 3.00e+00 1.11e-01 4.20e+00 angle pdb=" C PHE A 32 " pdb=" N THR A 33 " pdb=" CA THR A 33 " ideal model delta sigma weight residual 122.68 125.62 -2.94 1.47e+00 4.63e-01 4.01e+00 ... (remaining 4991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 2034 17.30 - 34.60: 135 34.60 - 51.90: 33 51.90 - 69.20: 8 69.20 - 86.49: 3 Dihedral angle restraints: 2213 sinusoidal: 922 harmonic: 1291 Sorted by residual: dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual -86.00 -135.37 49.37 1 1.00e+01 1.00e-02 3.35e+01 dihedral pdb=" CA ASN A 99 " pdb=" C ASN A 99 " pdb=" N ILE A 100 " pdb=" CA ILE A 100 " ideal model delta harmonic sigma weight residual 180.00 156.53 23.47 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA THR A 167 " pdb=" C THR A 167 " pdb=" N PHE A 168 " pdb=" CA PHE A 168 " ideal model delta harmonic sigma weight residual -180.00 -157.25 -22.75 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 2210 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 503 0.082 - 0.164: 60 0.164 - 0.246: 0 0.246 - 0.328: 1 0.328 - 0.410: 1 Chirality restraints: 565 Sorted by residual: chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA ILE L 49 " pdb=" N ILE L 49 " pdb=" C ILE L 49 " pdb=" CB ILE L 49 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.27e-01 ... (remaining 562 not shown) Planarity restraints: 637 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG L 55 " 0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO L 56 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO L 56 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO L 56 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 99 " -0.006 2.00e-02 2.50e+03 1.21e-02 1.46e+00 pdb=" C ASN A 99 " 0.021 2.00e-02 2.50e+03 pdb=" O ASN A 99 " -0.008 2.00e-02 2.50e+03 pdb=" N ILE A 100 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 61 " -0.010 2.00e-02 2.50e+03 9.87e-03 1.22e+00 pdb=" CG ASN A 61 " 0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN A 61 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 61 " 0.013 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " -0.011 2.00e-02 2.50e+03 ... (remaining 634 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 512 2.76 - 3.30: 3344 3.30 - 3.83: 4986 3.83 - 4.37: 5454 4.37 - 4.90: 10160 Nonbonded interactions: 24456 Sorted by model distance: nonbonded pdb=" OG SER L 68 " pdb=" OG SER L 71 " model vdw 2.225 3.040 nonbonded pdb=" O GLY L 30 " pdb=" NZ LYS L 67 " model vdw 2.273 3.120 nonbonded pdb=" OG1 THR A 109 " pdb=" OD1 ASP A 111 " model vdw 2.300 3.040 nonbonded pdb=" NZ LYS A 129 " pdb=" O PHE A 168 " model vdw 2.337 3.120 nonbonded pdb=" OG1 THR A 124 " pdb=" O7 NAG A1301 " model vdw 2.337 3.040 ... (remaining 24451 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: 6.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.720 Find NCS groups from input model: 0.040 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 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 : 0.003 0.033 3676 Z= 0.209 Angle : 0.656 7.544 4996 Z= 0.331 Chirality : 0.052 0.410 565 Planarity : 0.004 0.030 632 Dihedral : 12.810 86.494 1377 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.98 (0.38), residues: 438 helix: None (None), residues: 0 sheet: -0.01 (0.42), residues: 141 loop : -2.13 (0.33), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 108 HIS 0.001 0.000 HIS A 69 PHE 0.012 0.001 PHE A 238 TYR 0.010 0.001 TYR B 27 ARG 0.007 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.451 Fit side-chains REVERT: A 69 HIS cc_start: 0.7608 (t-90) cc_final: 0.7232 (t-90) REVERT: A 128 ILE cc_start: 0.8539 (mp) cc_final: 0.8327 (mp) REVERT: A 144 TYR cc_start: 0.8296 (p90) cc_final: 0.8091 (p90) REVERT: A 202 LYS cc_start: 0.8636 (mtpt) cc_final: 0.8367 (mtpt) REVERT: B 64 PHE cc_start: 0.8333 (m-10) cc_final: 0.8057 (m-10) REVERT: B 107 ASN cc_start: 0.7869 (p0) cc_final: 0.7609 (p0) REVERT: L 76 ILE cc_start: 0.8006 (tp) cc_final: 0.7749 (tt) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1853 time to fit residues: 23.4708 Evaluate side-chains 94 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 34 optimal weight: 0.0040 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 99 ASN A 196 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3676 Z= 0.291 Angle : 0.707 8.792 4996 Z= 0.369 Chirality : 0.055 0.543 565 Planarity : 0.005 0.033 632 Dihedral : 7.729 58.372 587 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.31 % Allowed : 11.83 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.74 (0.38), residues: 438 helix: None (None), residues: 0 sheet: 0.45 (0.42), residues: 144 loop : -2.17 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 108 HIS 0.003 0.001 HIS B 35 PHE 0.018 0.002 PHE A 86 TYR 0.015 0.002 TYR B 27 ARG 0.008 0.001 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.442 Fit side-chains REVERT: A 128 ILE cc_start: 0.8570 (mp) cc_final: 0.8278 (mp) REVERT: A 172 SER cc_start: 0.7712 (t) cc_final: 0.6952 (m) REVERT: A 202 LYS cc_start: 0.8615 (mtpt) cc_final: 0.8305 (mtpt) REVERT: B 107 ASN cc_start: 0.7903 (p0) cc_final: 0.7623 (p0) REVERT: L 55 ARG cc_start: 0.7355 (ptm160) cc_final: 0.7075 (ptm160) outliers start: 9 outliers final: 4 residues processed: 101 average time/residue: 0.1873 time to fit residues: 22.5700 Evaluate side-chains 96 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 250 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 11 optimal weight: 0.2980 chunk 40 optimal weight: 0.9980 chunk 43 optimal weight: 0.0870 chunk 35 optimal weight: 0.0970 chunk 39 optimal weight: 0.5980 chunk 13 optimal weight: 0.0770 chunk 32 optimal weight: 0.5980 overall best weight: 0.2314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** B 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 ASN L 32 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3676 Z= 0.163 Angle : 0.629 8.080 4996 Z= 0.326 Chirality : 0.051 0.445 565 Planarity : 0.005 0.036 632 Dihedral : 7.496 59.899 587 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.31 % Allowed : 14.14 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.49 (0.38), residues: 438 helix: None (None), residues: 0 sheet: 0.58 (0.41), residues: 152 loop : -2.03 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 92 HIS 0.001 0.000 HIS B 35 PHE 0.009 0.001 PHE A 92 TYR 0.008 0.001 TYR B 27 ARG 0.008 0.001 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.421 Fit side-chains REVERT: A 34 ARG cc_start: 0.7554 (mmm160) cc_final: 0.7133 (tpt90) REVERT: A 128 ILE cc_start: 0.8547 (mp) cc_final: 0.8281 (mp) REVERT: A 202 LYS cc_start: 0.8557 (mtpt) cc_final: 0.8243 (mtpt) REVERT: B 31 GLU cc_start: 0.8031 (pm20) cc_final: 0.7827 (pm20) REVERT: B 107 ASN cc_start: 0.7894 (p0) cc_final: 0.7556 (p0) REVERT: L 54 LYS cc_start: 0.8218 (ttmm) cc_final: 0.7923 (tppt) REVERT: L 76 ILE cc_start: 0.7950 (tp) cc_final: 0.7672 (tt) outliers start: 9 outliers final: 5 residues processed: 105 average time/residue: 0.1823 time to fit residues: 22.8389 Evaluate side-chains 96 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain L residue 23 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 0.0040 chunk 30 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 0.0970 chunk 19 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 40 optimal weight: 0.3980 chunk 42 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 chunk 11 optimal weight: 0.0570 chunk 35 optimal weight: 0.0670 overall best weight: 0.1246 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3676 Z= 0.138 Angle : 0.603 8.404 4996 Z= 0.307 Chirality : 0.048 0.408 565 Planarity : 0.004 0.030 632 Dihedral : 6.926 59.805 587 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.08 % Allowed : 14.65 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.34 (0.40), residues: 438 helix: None (None), residues: 0 sheet: 0.52 (0.39), residues: 173 loop : -2.00 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 104 HIS 0.002 0.000 HIS B 35 PHE 0.008 0.001 PHE A 92 TYR 0.010 0.001 TYR A 145 ARG 0.006 0.001 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.387 Fit side-chains REVERT: A 172 SER cc_start: 0.7337 (t) cc_final: 0.6749 (m) REVERT: A 195 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8570 (ttpp) REVERT: A 202 LYS cc_start: 0.8508 (mtpt) cc_final: 0.8211 (mtpt) REVERT: A 218 GLN cc_start: 0.8089 (pp30) cc_final: 0.7696 (tm-30) REVERT: B 59 ILE cc_start: 0.8248 (tp) cc_final: 0.7978 (mt) REVERT: B 72 GLU cc_start: 0.8017 (mp0) cc_final: 0.7681 (mp0) REVERT: B 81 MET cc_start: 0.8595 (tmm) cc_final: 0.8375 (ttm) REVERT: L 33 TYR cc_start: 0.7787 (m-80) cc_final: 0.6730 (m-80) REVERT: L 93 ASP cc_start: 0.9053 (t0) cc_final: 0.8757 (t0) outliers start: 12 outliers final: 5 residues processed: 105 average time/residue: 0.1878 time to fit residues: 23.3798 Evaluate side-chains 101 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain L residue 23 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 3676 Z= 0.395 Angle : 0.746 7.237 4996 Z= 0.394 Chirality : 0.056 0.576 565 Planarity : 0.005 0.034 632 Dihedral : 7.496 59.763 587 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.60 % Allowed : 16.45 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.40 (0.39), residues: 438 helix: None (None), residues: 0 sheet: 0.60 (0.38), residues: 167 loop : -2.08 (0.36), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 112 HIS 0.005 0.001 HIS B 35 PHE 0.022 0.002 PHE A 86 TYR 0.017 0.002 TYR B 95 ARG 0.004 0.001 ARG L 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.510 Fit side-chains REVERT: A 195 LYS cc_start: 0.8923 (ttpt) cc_final: 0.8624 (ttpp) REVERT: A 202 LYS cc_start: 0.8669 (mtpt) cc_final: 0.8283 (mtpt) REVERT: B 81 MET cc_start: 0.8683 (tmm) cc_final: 0.8414 (ttm) outliers start: 14 outliers final: 10 residues processed: 100 average time/residue: 0.2012 time to fit residues: 23.8675 Evaluate side-chains 105 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain L residue 23 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 35 optimal weight: 0.0170 chunk 19 optimal weight: 0.6980 chunk 3 optimal weight: 0.0030 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.0980 chunk 41 optimal weight: 0.6980 chunk 4 optimal weight: 0.4980 chunk 31 optimal weight: 0.0870 overall best weight: 0.1406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN B 107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3676 Z= 0.165 Angle : 0.668 8.229 4996 Z= 0.342 Chirality : 0.048 0.420 565 Planarity : 0.004 0.028 632 Dihedral : 6.821 59.487 587 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.57 % Allowed : 18.77 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.21 (0.40), residues: 438 helix: None (None), residues: 0 sheet: 0.90 (0.41), residues: 153 loop : -1.93 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 104 HIS 0.002 0.001 HIS A 146 PHE 0.009 0.001 PHE A 92 TYR 0.009 0.001 TYR A 145 ARG 0.008 0.001 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.411 Fit side-chains REVERT: A 195 LYS cc_start: 0.8855 (ttpt) cc_final: 0.8505 (ttpp) REVERT: A 202 LYS cc_start: 0.8597 (mtpt) cc_final: 0.8244 (mtpt) REVERT: A 218 GLN cc_start: 0.7511 (tm-30) cc_final: 0.7159 (pp30) REVERT: B 81 MET cc_start: 0.8443 (tmm) cc_final: 0.7881 (ttm) REVERT: L 76 ILE cc_start: 0.7797 (tp) cc_final: 0.7522 (tt) REVERT: L 93 ASP cc_start: 0.9043 (t0) cc_final: 0.8667 (t0) outliers start: 10 outliers final: 8 residues processed: 104 average time/residue: 0.1950 time to fit residues: 24.0686 Evaluate side-chains 107 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain L residue 108 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.5980 chunk 35 optimal weight: 0.0770 chunk 23 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 19 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 196 ASN ** B 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3676 Z= 0.256 Angle : 0.699 9.473 4996 Z= 0.361 Chirality : 0.052 0.507 565 Planarity : 0.005 0.031 632 Dihedral : 6.941 59.853 587 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 3.86 % Allowed : 18.77 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.20 (0.40), residues: 438 helix: None (None), residues: 0 sheet: 0.88 (0.41), residues: 154 loop : -1.92 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 112 HIS 0.003 0.001 HIS B 35 PHE 0.013 0.002 PHE A 86 TYR 0.011 0.001 TYR B 95 ARG 0.004 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.430 Fit side-chains REVERT: A 195 LYS cc_start: 0.8918 (ttpt) cc_final: 0.8679 (ttpp) REVERT: A 202 LYS cc_start: 0.8656 (mtpt) cc_final: 0.8272 (mtpt) REVERT: B 34 MET cc_start: 0.8138 (tpp) cc_final: 0.7618 (mmm) REVERT: B 81 MET cc_start: 0.8306 (tmm) cc_final: 0.8093 (ttm) REVERT: L 62 ARG cc_start: 0.7166 (mmt180) cc_final: 0.6640 (mmp80) REVERT: L 93 ASP cc_start: 0.9137 (t0) cc_final: 0.8837 (t0) outliers start: 15 outliers final: 9 residues processed: 103 average time/residue: 0.1994 time to fit residues: 24.3913 Evaluate side-chains 104 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain L residue 23 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 0.2980 chunk 3 optimal weight: 0.5980 chunk 33 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 23 optimal weight: 0.3980 chunk 17 optimal weight: 0.0770 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3676 Z= 0.227 Angle : 0.692 9.737 4996 Z= 0.357 Chirality : 0.051 0.485 565 Planarity : 0.004 0.030 632 Dihedral : 6.889 59.475 587 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.31 % Allowed : 19.28 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.21 (0.40), residues: 438 helix: None (None), residues: 0 sheet: 0.76 (0.42), residues: 151 loop : -1.82 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 112 HIS 0.002 0.001 HIS B 35 PHE 0.010 0.002 PHE A 86 TYR 0.010 0.001 TYR B 95 ARG 0.004 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.438 Fit side-chains REVERT: A 187 LYS cc_start: 0.7040 (mmmt) cc_final: 0.6725 (mmmm) REVERT: A 195 LYS cc_start: 0.8870 (ttpt) cc_final: 0.8638 (ttpp) REVERT: A 202 LYS cc_start: 0.8648 (mtpt) cc_final: 0.8275 (mtpt) REVERT: A 218 GLN cc_start: 0.7627 (tm-30) cc_final: 0.7177 (pp30) REVERT: B 34 MET cc_start: 0.8070 (tpp) cc_final: 0.7567 (mmm) REVERT: B 81 MET cc_start: 0.8357 (tmm) cc_final: 0.8046 (ttm) REVERT: L 55 ARG cc_start: 0.7007 (ttm170) cc_final: 0.6706 (ttt-90) REVERT: L 62 ARG cc_start: 0.7182 (mmt180) cc_final: 0.6570 (mmp-170) REVERT: L 93 ASP cc_start: 0.9115 (t0) cc_final: 0.8838 (t0) outliers start: 9 outliers final: 8 residues processed: 101 average time/residue: 0.1947 time to fit residues: 23.2172 Evaluate side-chains 105 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain L residue 23 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 0.0870 chunk 37 optimal weight: 0.3980 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3676 Z= 0.287 Angle : 0.734 9.835 4996 Z= 0.380 Chirality : 0.053 0.523 565 Planarity : 0.005 0.033 632 Dihedral : 7.172 59.677 587 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.06 % Allowed : 21.34 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.32 (0.40), residues: 438 helix: None (None), residues: 0 sheet: 0.68 (0.42), residues: 158 loop : -1.96 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 112 HIS 0.003 0.001 HIS B 35 PHE 0.015 0.002 PHE A 86 TYR 0.013 0.001 TYR B 95 ARG 0.004 0.001 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.424 Fit side-chains REVERT: A 195 LYS cc_start: 0.8848 (ttpt) cc_final: 0.8604 (ttpp) REVERT: A 202 LYS cc_start: 0.8703 (mtpt) cc_final: 0.8316 (mtpt) REVERT: B 34 MET cc_start: 0.8101 (tpp) cc_final: 0.7611 (mmm) REVERT: B 81 MET cc_start: 0.8237 (tmm) cc_final: 0.7919 (ttm) REVERT: L 62 ARG cc_start: 0.7230 (mmt180) cc_final: 0.6702 (mmp80) REVERT: L 76 ILE cc_start: 0.7942 (tp) cc_final: 0.7630 (tt) REVERT: L 93 ASP cc_start: 0.9133 (t0) cc_final: 0.8918 (t0) outliers start: 8 outliers final: 7 residues processed: 101 average time/residue: 0.1948 time to fit residues: 23.2812 Evaluate side-chains 104 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 2 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 0.0970 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 32 optimal weight: 0.1980 chunk 5 optimal weight: 0.4980 chunk 9 optimal weight: 0.3980 chunk 34 optimal weight: 0.9990 chunk 14 optimal weight: 0.2980 chunk 35 optimal weight: 0.0050 overall best weight: 0.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3676 Z= 0.182 Angle : 0.694 9.857 4996 Z= 0.354 Chirality : 0.050 0.436 565 Planarity : 0.004 0.030 632 Dihedral : 6.716 59.800 587 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.80 % Allowed : 21.59 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.19 (0.41), residues: 438 helix: None (None), residues: 0 sheet: 0.64 (0.40), residues: 177 loop : -1.95 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 104 HIS 0.001 0.000 HIS A 146 PHE 0.009 0.001 PHE A 92 TYR 0.010 0.001 TYR A 145 ARG 0.004 0.001 ARG L 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.392 Fit side-chains REVERT: A 187 LYS cc_start: 0.6884 (mmmt) cc_final: 0.6678 (mmmt) REVERT: A 195 LYS cc_start: 0.8674 (ttpt) cc_final: 0.8404 (ttpp) REVERT: A 202 LYS cc_start: 0.8644 (mtpt) cc_final: 0.8283 (mtpt) REVERT: B 34 MET cc_start: 0.7992 (tpp) cc_final: 0.7502 (mmm) REVERT: B 81 MET cc_start: 0.8258 (tmm) cc_final: 0.7943 (ttm) REVERT: L 62 ARG cc_start: 0.7095 (mmt180) cc_final: 0.6764 (mmt-90) REVERT: L 76 ILE cc_start: 0.7833 (tp) cc_final: 0.7543 (tt) REVERT: L 93 ASP cc_start: 0.9070 (t0) cc_final: 0.8799 (t0) outliers start: 7 outliers final: 7 residues processed: 100 average time/residue: 0.2072 time to fit residues: 24.8861 Evaluate side-chains 101 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 2 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 40 optimal weight: 0.0010 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 1 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 = 0.3614 r_free = 0.3614 target = 0.102590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.085575 restraints weight = 8826.125| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 4.21 r_work: 0.3196 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3676 Z= 0.292 Angle : 0.748 9.612 4996 Z= 0.385 Chirality : 0.053 0.518 565 Planarity : 0.004 0.034 632 Dihedral : 6.995 59.446 587 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.57 % Allowed : 21.59 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.32 (0.40), residues: 438 helix: None (None), residues: 0 sheet: 0.81 (0.43), residues: 151 loop : -1.98 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 36 HIS 0.003 0.001 HIS B 35 PHE 0.015 0.002 PHE A 86 TYR 0.012 0.002 TYR B 27 ARG 0.002 0.001 ARG A 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1625.62 seconds wall clock time: 30 minutes 43.80 seconds (1843.80 seconds total)