Starting phenix.real_space_refine on Mon Sep 23 16:18:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v24_31636/09_2024/7v24_31636.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v24_31636/09_2024/7v24_31636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v24_31636/09_2024/7v24_31636.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v24_31636/09_2024/7v24_31636.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v24_31636/09_2024/7v24_31636.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v24_31636/09_2024/7v24_31636.cif" } resolution = 3.29 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= 0.053 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 14 5.16 5 C 2436 2.51 5 N 636 2.21 5 O 728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3814 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 938 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "L" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 780 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "A" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2096 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 14, 'TRANS': 243} Chain breaks: 1 Time building chain proxies: 3.25, per 1000 atoms: 0.85 Number of scatterers: 3814 At special positions: 0 Unit cell: (77.76, 76.68, 98.28, 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 728 8.00 N 636 7.00 C 2436 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.03 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=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 446.1 milliseconds 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 894 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 10 sheets defined 6.8% alpha, 44.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'H' and resid 26 through 32 removed outlier: 3.598A pdb=" N PHE H 29 " --> pdb=" O GLU H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.558A pdb=" N TYR H 110 " --> pdb=" O TRP H 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 30 Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.721A pdb=" N GLU L 82 " --> pdb=" O ALA L 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 79 No H-bonds generated for 'chain 'A' and resid 77 through 79' Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.568A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.528A pdb=" N TYR L 85 " --> pdb=" O THR L 101 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLN L 36 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU L 45 " --> pdb=" O GLN L 36 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.528A pdb=" N TYR L 85 " --> pdb=" O THR L 101 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.711A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.997A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.995A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA9, first strand: chain 'A' and resid 154 through 160 removed outlier: 9.883A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 11.165A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 10.310A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.016A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 9.194A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ARG A 246 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 154 through 160 removed outlier: 9.883A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 11.165A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 10.310A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.016A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 9.194A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ARG A 246 " --> pdb=" O VAL A 143 " (cutoff:3.500A) 139 hydrogen bonds defined for protein. 336 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: 0.99 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1209 1.34 - 1.47: 1061 1.47 - 1.59: 1626 1.59 - 1.71: 0 1.71 - 1.83: 19 Bond restraints: 3915 Sorted by residual: bond pdb=" CA SER A 151 " pdb=" CB SER A 151 " ideal model delta sigma weight residual 1.532 1.473 0.059 2.23e-02 2.01e+03 7.10e+00 bond pdb=" N SER A 151 " pdb=" CA SER A 151 " ideal model delta sigma weight residual 1.458 1.482 -0.024 1.00e-02 1.00e+04 5.83e+00 bond pdb=" N TRP A 152 " pdb=" CA TRP A 152 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.24e-02 6.50e+03 4.34e+00 bond pdb=" N LYS A 150 " pdb=" CA LYS A 150 " ideal model delta sigma weight residual 1.457 1.482 -0.024 1.29e-02 6.01e+03 3.58e+00 bond pdb=" N ASN A 149 " pdb=" CA ASN A 149 " ideal model delta sigma weight residual 1.463 1.486 -0.023 1.27e-02 6.20e+03 3.33e+00 ... (remaining 3910 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 5176 2.11 - 4.22: 131 4.22 - 6.32: 15 6.32 - 8.43: 1 8.43 - 10.54: 2 Bond angle restraints: 5325 Sorted by residual: angle pdb=" C ARG A 78 " pdb=" N PHE A 79 " pdb=" CA PHE A 79 " ideal model delta sigma weight residual 121.54 128.21 -6.67 1.91e+00 2.74e-01 1.22e+01 angle pdb=" N ALA A 123 " pdb=" CA ALA A 123 " pdb=" C ALA A 123 " ideal model delta sigma weight residual 114.62 110.69 3.93 1.14e+00 7.69e-01 1.19e+01 angle pdb=" CA TRP A 152 " pdb=" C TRP A 152 " pdb=" O TRP A 152 " ideal model delta sigma weight residual 120.55 117.08 3.47 1.07e+00 8.73e-01 1.05e+01 angle pdb=" N SER A 151 " pdb=" CA SER A 151 " pdb=" C SER A 151 " ideal model delta sigma weight residual 112.54 107.75 4.79 1.51e+00 4.39e-01 1.01e+01 angle pdb=" CA ALA A 123 " pdb=" C ALA A 123 " pdb=" N THR A 124 " ideal model delta sigma weight residual 119.71 116.08 3.63 1.17e+00 7.31e-01 9.63e+00 ... (remaining 5320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 2052 17.09 - 34.18: 195 34.18 - 51.27: 25 51.27 - 68.36: 4 68.36 - 85.45: 6 Dihedral angle restraints: 2282 sinusoidal: 878 harmonic: 1404 Sorted by residual: dihedral pdb=" CA PHE A 79 " pdb=" C PHE A 79 " pdb=" N ASP A 80 " pdb=" CA ASP A 80 " ideal model delta harmonic sigma weight residual 180.00 148.24 31.76 0 5.00e+00 4.00e-02 4.03e+01 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 93.00 49.29 43.71 1 1.00e+01 1.00e-02 2.66e+01 dihedral pdb=" CA THR A 95 " pdb=" C THR A 95 " pdb=" N GLU A 96 " pdb=" CA GLU A 96 " ideal model delta harmonic sigma weight residual 180.00 159.12 20.88 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 2279 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 423 0.048 - 0.095: 119 0.095 - 0.143: 33 0.143 - 0.191: 3 0.191 - 0.238: 2 Chirality restraints: 580 Sorted by residual: chirality pdb=" CG LEU A 216 " pdb=" CB LEU A 216 " pdb=" CD1 LEU A 216 " pdb=" CD2 LEU A 216 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB THR A 33 " pdb=" CA THR A 33 " pdb=" OG1 THR A 33 " pdb=" CG2 THR A 33 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA ASP A 80 " pdb=" N ASP A 80 " pdb=" C ASP A 80 " pdb=" CB ASP A 80 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.65e-01 ... (remaining 577 not shown) Planarity restraints: 682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO L 7 " -0.038 5.00e-02 4.00e+02 5.82e-02 5.43e+00 pdb=" N PRO L 8 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 266 " -0.011 2.00e-02 2.50e+03 1.61e-02 5.19e+00 pdb=" CG TYR A 266 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR A 266 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR A 266 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 266 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 266 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 266 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 266 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 250 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO A 251 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 251 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 251 " -0.023 5.00e-02 4.00e+02 ... (remaining 679 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 197 2.71 - 3.26: 3714 3.26 - 3.81: 6069 3.81 - 4.35: 7911 4.35 - 4.90: 13988 Nonbonded interactions: 31879 Sorted by model distance: nonbonded pdb=" OH TYR H 110 " pdb=" OH TYR A 144 " model vdw 2.164 3.040 nonbonded pdb=" OH TYR A 144 " pdb=" OE2 GLU A 156 " model vdw 2.166 3.040 nonbonded pdb=" O ASP A 80 " pdb=" OH TYR A 265 " model vdw 2.174 3.040 nonbonded pdb=" OG SER H 33 " pdb=" O GLY H 101 " model vdw 2.175 3.040 nonbonded pdb=" NE2 GLN H 39 " pdb=" O LYS H 43 " model vdw 2.196 3.120 ... (remaining 31874 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: 2.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.700 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 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 : 0.006 0.059 3915 Z= 0.405 Angle : 0.798 10.541 5325 Z= 0.452 Chirality : 0.049 0.238 580 Planarity : 0.005 0.058 682 Dihedral : 13.640 85.447 1376 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.27 % Favored : 88.73 % Rotamer: Outliers : 0.24 % Allowed : 0.24 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -1.86 (0.37), residues: 479 helix: -4.96 (0.48), residues: 6 sheet: -0.76 (0.40), residues: 164 loop : -1.47 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 47 HIS 0.003 0.001 HIS A 66 PHE 0.015 0.002 PHE A 86 TYR 0.038 0.002 TYR A 266 ARG 0.005 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 84 average time/residue: 0.2046 time to fit residues: 20.7273 Evaluate side-chains 66 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 23 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** H 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3915 Z= 0.300 Angle : 0.706 8.244 5325 Z= 0.365 Chirality : 0.047 0.185 580 Planarity : 0.005 0.051 682 Dihedral : 6.376 54.062 531 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer: Outliers : 0.71 % Allowed : 8.57 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.63 (0.38), residues: 479 helix: -5.17 (0.33), residues: 6 sheet: -0.49 (0.41), residues: 163 loop : -1.37 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.004 0.001 HIS A 207 PHE 0.013 0.002 PHE H 29 TYR 0.029 0.002 TYR A 266 ARG 0.003 0.001 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 46 GLU cc_start: 0.7716 (tt0) cc_final: 0.7381 (tt0) REVERT: H 57 GLN cc_start: 0.7042 (mm-40) cc_final: 0.6780 (mm-40) REVERT: A 41 LYS cc_start: 0.5748 (tptt) cc_final: 0.5174 (tptt) outliers start: 3 outliers final: 3 residues processed: 71 average time/residue: 0.1816 time to fit residues: 15.7620 Evaluate side-chains 61 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain A residue 276 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 13 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 38 optimal weight: 0.3980 chunk 14 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 3915 Z= 0.309 Angle : 0.681 7.178 5325 Z= 0.352 Chirality : 0.047 0.180 580 Planarity : 0.005 0.047 682 Dihedral : 5.605 28.543 529 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 3.10 % Allowed : 10.95 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.39), residues: 479 helix: -5.16 (0.33), residues: 6 sheet: -0.31 (0.39), residues: 180 loop : -1.17 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.002 0.001 HIS A 207 PHE 0.015 0.002 PHE H 29 TYR 0.021 0.002 TYR A 266 ARG 0.004 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 0.400 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 70 average time/residue: 0.1513 time to fit residues: 13.3469 Evaluate side-chains 60 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 276 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 3915 Z= 0.359 Angle : 0.673 7.247 5325 Z= 0.349 Chirality : 0.046 0.177 580 Planarity : 0.005 0.045 682 Dihedral : 5.515 28.397 529 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer: Outliers : 3.10 % Allowed : 10.95 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.38), residues: 479 helix: -5.15 (0.34), residues: 6 sheet: -0.37 (0.38), residues: 182 loop : -1.22 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.002 0.001 HIS A 207 PHE 0.014 0.002 PHE H 29 TYR 0.018 0.002 TYR A 266 ARG 0.002 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 0.428 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 70 average time/residue: 0.1486 time to fit residues: 13.1314 Evaluate side-chains 61 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 62 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 33 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 40 optimal weight: 0.0060 chunk 11 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3915 Z= 0.261 Angle : 0.631 7.257 5325 Z= 0.327 Chirality : 0.044 0.172 580 Planarity : 0.004 0.042 682 Dihedral : 5.345 28.344 529 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 3.10 % Allowed : 13.10 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.39), residues: 479 helix: -5.14 (0.34), residues: 6 sheet: -0.32 (0.39), residues: 179 loop : -1.12 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.002 0.001 HIS A 207 PHE 0.013 0.001 PHE H 29 TYR 0.014 0.002 TYR A 266 ARG 0.003 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 54 time to evaluate : 0.465 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 64 average time/residue: 0.1619 time to fit residues: 12.9598 Evaluate side-chains 60 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 52 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 208 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 11 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 0.0270 chunk 33 optimal weight: 0.8980 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 3915 Z= 0.309 Angle : 0.642 7.522 5325 Z= 0.332 Chirality : 0.045 0.171 580 Planarity : 0.004 0.042 682 Dihedral : 5.339 28.246 529 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 3.10 % Allowed : 15.00 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.38), residues: 479 helix: -5.15 (0.34), residues: 6 sheet: -0.34 (0.39), residues: 179 loop : -1.15 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.002 0.001 HIS A 207 PHE 0.013 0.001 PHE H 29 TYR 0.014 0.002 TYR H 95 ARG 0.002 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 56 time to evaluate : 0.428 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 67 average time/residue: 0.1454 time to fit residues: 12.4769 Evaluate side-chains 66 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 56 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 208 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 3915 Z= 0.324 Angle : 0.650 7.831 5325 Z= 0.336 Chirality : 0.045 0.168 580 Planarity : 0.004 0.041 682 Dihedral : 5.332 28.122 529 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 2.86 % Allowed : 16.43 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.27 (0.38), residues: 479 helix: -5.15 (0.34), residues: 6 sheet: -0.29 (0.38), residues: 179 loop : -1.11 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.002 0.001 HIS A 207 PHE 0.013 0.001 PHE H 29 TYR 0.014 0.002 TYR H 95 ARG 0.002 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 54 time to evaluate : 0.430 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 10 residues processed: 65 average time/residue: 0.1463 time to fit residues: 12.3402 Evaluate side-chains 63 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 53 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 208 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 3915 Z= 0.351 Angle : 0.662 8.459 5325 Z= 0.341 Chirality : 0.045 0.168 580 Planarity : 0.004 0.040 682 Dihedral : 5.380 28.198 529 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer: Outliers : 2.86 % Allowed : 16.19 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.38), residues: 479 helix: None (None), residues: 0 sheet: -0.35 (0.38), residues: 183 loop : -1.16 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.002 0.001 HIS A 207 PHE 0.013 0.002 PHE H 29 TYR 0.015 0.002 TYR H 95 ARG 0.002 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 56 time to evaluate : 0.450 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 10 residues processed: 67 average time/residue: 0.1555 time to fit residues: 13.1736 Evaluate side-chains 65 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 208 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 46 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3915 Z= 0.276 Angle : 0.636 8.401 5325 Z= 0.328 Chirality : 0.044 0.167 580 Planarity : 0.004 0.040 682 Dihedral : 5.300 28.013 529 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 2.62 % Allowed : 17.14 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.38), residues: 479 helix: None (None), residues: 0 sheet: -0.27 (0.38), residues: 182 loop : -1.11 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.002 0.001 HIS A 207 PHE 0.013 0.001 PHE H 29 TYR 0.014 0.002 TYR H 95 ARG 0.002 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 54 time to evaluate : 0.422 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 10 residues processed: 64 average time/residue: 0.1772 time to fit residues: 14.1022 Evaluate side-chains 61 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 51 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 208 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 39 optimal weight: 0.2980 chunk 11 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 5 optimal weight: 0.0870 chunk 10 optimal weight: 0.4980 chunk 37 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3915 Z= 0.213 Angle : 0.619 8.157 5325 Z= 0.319 Chirality : 0.044 0.168 580 Planarity : 0.004 0.039 682 Dihedral : 5.153 27.789 529 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 2.14 % Allowed : 18.10 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.39), residues: 479 helix: None (None), residues: 0 sheet: -0.07 (0.38), residues: 179 loop : -1.02 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.001 0.001 HIS A 207 PHE 0.013 0.001 PHE H 29 TYR 0.012 0.001 TYR H 95 ARG 0.002 0.000 ARG A 273 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.319 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 62 average time/residue: 0.1455 time to fit residues: 11.3662 Evaluate side-chains 57 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 208 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 6 optimal weight: 0.0170 chunk 32 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 1 optimal weight: 0.0470 chunk 29 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.118520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.094165 restraints weight = 5361.599| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.46 r_work: 0.2985 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3915 Z= 0.214 Angle : 0.611 8.265 5325 Z= 0.316 Chirality : 0.044 0.168 580 Planarity : 0.004 0.038 682 Dihedral : 5.080 27.696 529 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 2.38 % Allowed : 18.57 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.38), residues: 479 helix: None (None), residues: 0 sheet: -0.07 (0.38), residues: 180 loop : -1.02 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.001 0.001 HIS A 207 PHE 0.012 0.001 PHE H 29 TYR 0.012 0.001 TYR H 95 ARG 0.002 0.000 ARG A 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1403.67 seconds wall clock time: 29 minutes 10.00 seconds (1750.00 seconds total)