Starting phenix.real_space_refine on Mon Sep 23 16:11:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yp1_33992/09_2024/7yp1_33992.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yp1_33992/09_2024/7yp1_33992.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yp1_33992/09_2024/7yp1_33992.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yp1_33992/09_2024/7yp1_33992.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yp1_33992/09_2024/7yp1_33992.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yp1_33992/09_2024/7yp1_33992.cif" } resolution = 3.54 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= 0.013 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 17 5.16 5 C 2411 2.51 5 N 620 2.21 5 O 722 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 3770 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1482 Classifications: {'peptide': 185} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 173} Chain breaks: 3 Chain: "B" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 588 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "D" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 865 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "G" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 835 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 107} Time building chain proxies: 4.14, per 1000 atoms: 1.10 Number of scatterers: 3770 At special positions: 0 Unit cell: (83.246, 71.576, 87.136, 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 17 16.00 O 722 8.00 N 620 7.00 C 2411 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 93 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " 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: 0.83 Conformation dependent library (CDL) restraints added in 473.5 milliseconds 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 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: 11 helices and 10 sheets defined 16.9% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 42 through 47 removed outlier: 3.665A pdb=" N VAL A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 60 removed outlier: 3.690A pdb=" N TRP A 56 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ARG A 57 " --> pdb=" O GLU A 53 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN A 60 " --> pdb=" O TRP A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 73 removed outlier: 4.276A pdb=" N ARG A 71 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 131 removed outlier: 3.533A pdb=" N PHE A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'B' and resid 41 through 45 removed outlier: 3.928A pdb=" N ILE B 45 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.995A pdb=" N SER B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N SER B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 117 removed outlier: 3.667A pdb=" N LEU B 107 " --> pdb=" O HIS B 103 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 123 Processing helix chain 'D' and resid 84 through 88 removed outlier: 3.913A pdb=" N THR D 88 " --> pdb=" O THR D 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.694A pdb=" N ASP G 82 " --> pdb=" O GLU G 79 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALA G 83 " --> pdb=" O CYS G 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 79 through 83' Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 3.722A pdb=" N ILE B 48 " --> pdb=" O LYS A 24 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP A 28 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP B 47 " --> pdb=" O ASN B 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 135 through 138 removed outlier: 3.588A pdb=" N GLY A 135 " --> pdb=" O CYS A 153 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU A 151 " --> pdb=" O MET A 137 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 158 removed outlier: 3.568A pdb=" N MET A 173 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 177 through 182 removed outlier: 3.692A pdb=" N SER A 195 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TYR A 224 " --> pdb=" O GLN A 220 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLN A 220 " --> pdb=" O TYR A 224 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU A 226 " --> pdb=" O SER A 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 61 through 62 removed outlier: 4.087A pdb=" N ALA B 62 " --> pdb=" O ALA B 80 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AA7, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.819A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N MET D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.657A pdb=" N THR G 5 " --> pdb=" O GLN G 24 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN G 24 " --> pdb=" O THR G 5 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.538A pdb=" N VAL G 109 " --> pdb=" O VAL G 11 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 53 through 54 removed outlier: 6.616A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR G 87 " --> pdb=" O TYR G 36 " (cutoff:3.500A) 99 hydrogen bonds defined for protein. 240 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: 0.90 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 600 1.31 - 1.44: 1103 1.44 - 1.56: 2124 1.56 - 1.68: 2 1.68 - 1.81: 25 Bond restraints: 3854 Sorted by residual: bond pdb=" CA LEU G 73 " pdb=" C LEU G 73 " ideal model delta sigma weight residual 1.521 1.439 0.082 1.24e-02 6.50e+03 4.33e+01 bond pdb=" CA LYS G 63 " pdb=" C LYS G 63 " ideal model delta sigma weight residual 1.522 1.455 0.067 1.24e-02 6.50e+03 2.92e+01 bond pdb=" CA ILE G 75 " pdb=" CB ILE G 75 " ideal model delta sigma weight residual 1.538 1.490 0.048 9.80e-03 1.04e+04 2.43e+01 bond pdb=" C LEU G 73 " pdb=" O LEU G 73 " ideal model delta sigma weight residual 1.235 1.189 0.046 1.22e-02 6.72e+03 1.41e+01 bond pdb=" CA ILE G 75 " pdb=" C ILE G 75 " ideal model delta sigma weight residual 1.527 1.470 0.057 1.52e-02 4.33e+03 1.38e+01 ... (remaining 3849 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 4820 1.70 - 3.41: 314 3.41 - 5.11: 78 5.11 - 6.82: 12 6.82 - 8.52: 11 Bond angle restraints: 5235 Sorted by residual: angle pdb=" N GLY G 66 " pdb=" CA GLY G 66 " pdb=" C GLY G 66 " ideal model delta sigma weight residual 111.95 116.83 -4.88 9.50e-01 1.11e+00 2.64e+01 angle pdb=" CA THR G 72 " pdb=" C THR G 72 " pdb=" N LEU G 73 " ideal model delta sigma weight residual 115.61 122.80 -7.19 1.45e+00 4.76e-01 2.46e+01 angle pdb=" N LEU G 73 " pdb=" CA LEU G 73 " pdb=" C LEU G 73 " ideal model delta sigma weight residual 109.24 102.14 7.10 1.67e+00 3.59e-01 1.81e+01 angle pdb=" N THR G 69 " pdb=" CA THR G 69 " pdb=" C THR G 69 " ideal model delta sigma weight residual 113.17 118.02 -4.85 1.26e+00 6.30e-01 1.48e+01 angle pdb=" N TYR A 213 " pdb=" CA TYR A 213 " pdb=" C TYR A 213 " ideal model delta sigma weight residual 109.81 118.22 -8.41 2.21e+00 2.05e-01 1.45e+01 ... (remaining 5230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 2015 17.44 - 34.88: 198 34.88 - 52.32: 33 52.32 - 69.77: 3 69.77 - 87.21: 4 Dihedral angle restraints: 2253 sinusoidal: 850 harmonic: 1403 Sorted by residual: dihedral pdb=" CB CYS G 23 " pdb=" SG CYS G 23 " pdb=" SG CYS G 88 " pdb=" CB CYS G 88 " ideal model delta sinusoidal sigma weight residual 93.00 157.67 -64.67 1 1.00e+01 1.00e-02 5.49e+01 dihedral pdb=" CA TYR A 235 " pdb=" C TYR A 235 " pdb=" N ALA A 236 " pdb=" CA ALA A 236 " ideal model delta harmonic sigma weight residual 180.00 151.20 28.80 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA ASP A 248 " pdb=" C ASP A 248 " pdb=" N MET A 249 " pdb=" CA MET A 249 " ideal model delta harmonic sigma weight residual 180.00 155.26 24.74 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 2250 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 414 0.057 - 0.114: 150 0.114 - 0.171: 30 0.171 - 0.228: 7 0.228 - 0.285: 3 Chirality restraints: 604 Sorted by residual: chirality pdb=" CA ARG G 61 " pdb=" N ARG G 61 " pdb=" C ARG G 61 " pdb=" CB ARG G 61 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA THR G 69 " pdb=" N THR G 69 " pdb=" C THR G 69 " pdb=" CB THR G 69 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CB THR A 181 " pdb=" CA THR A 181 " pdb=" OG1 THR A 181 " pdb=" CG2 THR A 181 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 601 not shown) Planarity restraints: 652 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 124 " -0.048 5.00e-02 4.00e+02 7.23e-02 8.36e+00 pdb=" N PRO A 125 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 125 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 125 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 102 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.14e+00 pdb=" C ARG D 102 " 0.043 2.00e-02 2.50e+03 pdb=" O ARG D 102 " -0.016 2.00e-02 2.50e+03 pdb=" N PHE D 103 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS G 39 " -0.037 5.00e-02 4.00e+02 5.62e-02 5.06e+00 pdb=" N PRO G 40 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO G 40 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO G 40 " -0.031 5.00e-02 4.00e+02 ... (remaining 649 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1106 2.80 - 3.33: 2870 3.33 - 3.85: 5796 3.85 - 4.38: 6517 4.38 - 4.90: 12039 Nonbonded interactions: 28328 Sorted by model distance: nonbonded pdb=" O SER A 251 " pdb=" OG SER A 251 " model vdw 2.275 3.040 nonbonded pdb=" O SER B 87 " pdb=" OG SER B 87 " model vdw 2.289 3.040 nonbonded pdb=" OG1 THR A 201 " pdb=" O ASP A 223 " model vdw 2.302 3.040 nonbonded pdb=" O PHE A 211 " pdb=" OH TYR B 115 " model vdw 2.314 3.040 nonbonded pdb=" O SER B 96 " pdb=" OG SER B 96 " model vdw 2.339 3.040 ... (remaining 28323 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.430 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.810 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 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 : 0.010 0.082 3854 Z= 0.686 Angle : 1.055 8.520 5235 Z= 0.591 Chirality : 0.065 0.285 604 Planarity : 0.007 0.072 652 Dihedral : 14.046 87.208 1353 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 0.24 % Allowed : 11.81 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % 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: -5.19 (0.30), residues: 474 helix: -5.07 (0.16), residues: 84 sheet: -2.38 (0.40), residues: 151 loop : -3.56 (0.31), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP D 33 HIS 0.008 0.002 HIS A 192 PHE 0.021 0.003 PHE A 177 TYR 0.017 0.002 TYR A 132 ARG 0.006 0.001 ARG D 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 0.451 Fit side-chains REVERT: B 78 ARG cc_start: 0.7685 (mmt180) cc_final: 0.6756 (mmm160) outliers start: 1 outliers final: 0 residues processed: 74 average time/residue: 0.2296 time to fit residues: 19.9537 Evaluate side-chains 65 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 0.2980 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3854 Z= 0.238 Angle : 0.606 6.950 5235 Z= 0.320 Chirality : 0.045 0.154 604 Planarity : 0.005 0.041 652 Dihedral : 5.917 44.346 530 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 1.69 % Allowed : 16.39 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % 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: -4.27 (0.33), residues: 474 helix: -4.22 (0.29), residues: 88 sheet: -1.75 (0.43), residues: 154 loop : -3.01 (0.33), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 33 HIS 0.003 0.001 HIS A 192 PHE 0.007 0.001 PHE B 89 TYR 0.010 0.001 TYR D 47 ARG 0.002 0.000 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.435 Fit side-chains REVERT: B 78 ARG cc_start: 0.7711 (mmt180) cc_final: 0.6758 (mmm160) outliers start: 7 outliers final: 5 residues processed: 72 average time/residue: 0.2243 time to fit residues: 19.0665 Evaluate side-chains 67 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain D residue 64 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 34 optimal weight: 0.0870 chunk 32 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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: 0.8143 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3854 Z= 0.285 Angle : 0.580 6.865 5235 Z= 0.305 Chirality : 0.045 0.154 604 Planarity : 0.004 0.031 652 Dihedral : 5.568 39.161 530 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 4.34 % Allowed : 17.59 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % 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: -3.80 (0.35), residues: 474 helix: -3.61 (0.38), residues: 90 sheet: -1.54 (0.43), residues: 156 loop : -2.73 (0.36), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 33 HIS 0.003 0.001 HIS A 192 PHE 0.010 0.001 PHE A 177 TYR 0.011 0.001 TYR G 92 ARG 0.002 0.000 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 63 time to evaluate : 0.428 Fit side-chains REVERT: A 179 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7563 (ttt) REVERT: B 78 ARG cc_start: 0.7729 (mmt180) cc_final: 0.6765 (mmm160) REVERT: D 29 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8438 (pp) REVERT: D 80 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.7983 (mt) outliers start: 18 outliers final: 8 residues processed: 77 average time/residue: 0.1955 time to fit residues: 18.0818 Evaluate side-chains 74 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 63 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain D residue 2 GLN Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 113 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 0.0570 chunk 20 optimal weight: 0.0040 chunk 28 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 40 optimal weight: 0.2980 chunk 12 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.3710 ------------------------------------------------------------------------------- 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: 0.8104 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3854 Z= 0.177 Angle : 0.518 6.072 5235 Z= 0.272 Chirality : 0.042 0.143 604 Planarity : 0.004 0.033 652 Dihedral : 5.133 33.781 530 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.41 % Allowed : 20.96 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % 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: -3.31 (0.36), residues: 474 helix: -3.17 (0.44), residues: 90 sheet: -1.14 (0.44), residues: 155 loop : -2.50 (0.37), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 33 HIS 0.002 0.001 HIS A 26 PHE 0.008 0.001 PHE A 177 TYR 0.009 0.001 TYR D 47 ARG 0.001 0.000 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 0.418 Fit side-chains REVERT: A 179 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7546 (ttt) REVERT: A 248 ASP cc_start: 0.8087 (m-30) cc_final: 0.7586 (t70) REVERT: B 78 ARG cc_start: 0.7713 (mmt180) cc_final: 0.6752 (mmm160) outliers start: 10 outliers final: 8 residues processed: 74 average time/residue: 0.2036 time to fit residues: 17.9805 Evaluate side-chains 70 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain G residue 101 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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: 0.8186 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 3854 Z= 0.444 Angle : 0.640 7.058 5235 Z= 0.332 Chirality : 0.048 0.159 604 Planarity : 0.004 0.032 652 Dihedral : 5.692 41.277 530 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 4.34 % Allowed : 20.00 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % 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: -3.26 (0.36), residues: 474 helix: -3.13 (0.45), residues: 90 sheet: -1.08 (0.43), residues: 155 loop : -2.51 (0.37), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 33 HIS 0.004 0.001 HIS A 192 PHE 0.014 0.002 PHE B 89 TYR 0.012 0.002 TYR D 47 ARG 0.003 0.000 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 65 time to evaluate : 0.407 Fit side-chains REVERT: A 137 MET cc_start: 0.8970 (tpt) cc_final: 0.8713 (tpt) REVERT: A 179 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7617 (ttt) REVERT: A 184 ARG cc_start: 0.7027 (ttp80) cc_final: 0.6647 (mmt180) REVERT: B 78 ARG cc_start: 0.7752 (mmt180) cc_final: 0.6784 (mmm160) REVERT: D 29 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8473 (pp) outliers start: 18 outliers final: 12 residues processed: 76 average time/residue: 0.2124 time to fit residues: 19.1100 Evaluate side-chains 78 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 64 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain D residue 2 GLN Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain G residue 101 ASP 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: 0.9990 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8156 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3854 Z= 0.293 Angle : 0.569 6.549 5235 Z= 0.296 Chirality : 0.044 0.149 604 Planarity : 0.004 0.034 652 Dihedral : 5.424 37.377 530 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 3.86 % Allowed : 21.45 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % 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: -3.06 (0.37), residues: 474 helix: -2.93 (0.47), residues: 89 sheet: -0.89 (0.44), residues: 155 loop : -2.46 (0.38), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 33 HIS 0.002 0.001 HIS A 192 PHE 0.010 0.001 PHE A 177 TYR 0.014 0.001 TYR A 213 ARG 0.002 0.000 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 64 time to evaluate : 0.425 Fit side-chains REVERT: A 137 MET cc_start: 0.8932 (tpt) cc_final: 0.8660 (tpt) REVERT: A 179 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7525 (ttt) REVERT: A 184 ARG cc_start: 0.7046 (ttp80) cc_final: 0.6591 (mmt180) REVERT: B 78 ARG cc_start: 0.7752 (mmt180) cc_final: 0.6790 (mmm160) REVERT: D 29 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8493 (pp) outliers start: 16 outliers final: 12 residues processed: 75 average time/residue: 0.1992 time to fit residues: 17.9140 Evaluate side-chains 78 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 64 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain D residue 2 GLN Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain G residue 11 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 45 optimal weight: 0.3980 chunk 28 optimal weight: 0.9990 chunk 27 optimal weight: 0.1980 chunk 20 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.2980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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: 0.8118 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3854 Z= 0.196 Angle : 0.522 7.166 5235 Z= 0.271 Chirality : 0.042 0.142 604 Planarity : 0.003 0.031 652 Dihedral : 4.993 31.811 530 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 4.10 % Allowed : 21.69 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % 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: -2.84 (0.38), residues: 474 helix: -2.74 (0.49), residues: 90 sheet: -0.71 (0.44), residues: 155 loop : -2.35 (0.39), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 33 HIS 0.003 0.001 HIS A 26 PHE 0.008 0.001 PHE A 177 TYR 0.009 0.001 TYR G 49 ARG 0.001 0.000 ARG D 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 66 time to evaluate : 0.423 Fit side-chains REVERT: A 179 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7547 (ttt) REVERT: A 184 ARG cc_start: 0.6961 (ttp80) cc_final: 0.6499 (mmt180) REVERT: A 232 PHE cc_start: 0.7831 (OUTLIER) cc_final: 0.7460 (t80) REVERT: A 249 MET cc_start: 0.8386 (mtt) cc_final: 0.8184 (mtm) REVERT: B 78 ARG cc_start: 0.7748 (mmt180) cc_final: 0.6791 (mmm160) REVERT: D 29 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8507 (pp) outliers start: 17 outliers final: 12 residues processed: 78 average time/residue: 0.2002 time to fit residues: 18.7752 Evaluate side-chains 79 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 64 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain D residue 2 GLN Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain G residue 11 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 0.0470 chunk 35 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 12 optimal weight: 0.0980 chunk 38 optimal weight: 1.9990 overall best weight: 0.3278 ------------------------------------------------------------------------------- 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: 0.8098 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3854 Z= 0.163 Angle : 0.502 6.806 5235 Z= 0.261 Chirality : 0.042 0.140 604 Planarity : 0.003 0.032 652 Dihedral : 4.797 29.282 530 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.61 % Allowed : 23.13 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % 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: -2.68 (0.38), residues: 474 helix: -2.57 (0.50), residues: 91 sheet: -0.61 (0.45), residues: 149 loop : -2.22 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 33 HIS 0.002 0.001 HIS A 26 PHE 0.009 0.001 PHE A 177 TYR 0.010 0.001 TYR A 213 ARG 0.001 0.000 ARG D 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 67 time to evaluate : 0.419 Fit side-chains REVERT: A 179 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7571 (ttt) REVERT: A 184 ARG cc_start: 0.6945 (ttp80) cc_final: 0.6472 (mmt180) REVERT: A 232 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.7495 (t80) REVERT: B 78 ARG cc_start: 0.7732 (mmt180) cc_final: 0.6745 (mmm160) REVERT: D 29 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8466 (pp) outliers start: 15 outliers final: 10 residues processed: 77 average time/residue: 0.2042 time to fit residues: 18.6567 Evaluate side-chains 78 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain D residue 2 GLN Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain G residue 11 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 0.5980 chunk 42 optimal weight: 0.0060 chunk 27 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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: 0.8115 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 3854 Z= 0.241 Angle : 0.539 6.969 5235 Z= 0.281 Chirality : 0.043 0.197 604 Planarity : 0.003 0.031 652 Dihedral : 4.867 31.584 530 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 4.10 % Allowed : 22.17 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % 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: -2.63 (0.38), residues: 474 helix: -2.53 (0.50), residues: 91 sheet: -0.59 (0.45), residues: 149 loop : -2.19 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 33 HIS 0.002 0.001 HIS A 26 PHE 0.012 0.001 PHE A 177 TYR 0.009 0.001 TYR D 47 ARG 0.001 0.000 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 63 time to evaluate : 0.426 Fit side-chains REVERT: A 179 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7545 (ttt) REVERT: A 184 ARG cc_start: 0.6956 (ttp80) cc_final: 0.6519 (mmt180) REVERT: A 232 PHE cc_start: 0.7866 (OUTLIER) cc_final: 0.7488 (t80) REVERT: B 78 ARG cc_start: 0.7721 (mmt180) cc_final: 0.6781 (mmm160) REVERT: D 29 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8465 (pp) outliers start: 17 outliers final: 12 residues processed: 74 average time/residue: 0.2137 time to fit residues: 18.7821 Evaluate side-chains 78 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 63 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain D residue 2 GLN Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 21 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 0.0970 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 0.0770 overall best weight: 0.5536 ------------------------------------------------------------------------------- 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: 0.8121 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 3854 Z= 0.235 Angle : 0.538 7.036 5235 Z= 0.280 Chirality : 0.043 0.145 604 Planarity : 0.003 0.031 652 Dihedral : 4.933 33.128 530 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.86 % Allowed : 22.41 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % 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: -2.56 (0.38), residues: 474 helix: -2.45 (0.51), residues: 91 sheet: -0.58 (0.45), residues: 149 loop : -2.12 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 33 HIS 0.002 0.001 HIS A 26 PHE 0.012 0.001 PHE A 177 TYR 0.009 0.001 TYR A 182 ARG 0.001 0.000 ARG D 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 64 time to evaluate : 0.427 Fit side-chains REVERT: A 179 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7539 (ttt) REVERT: A 184 ARG cc_start: 0.6885 (ttp80) cc_final: 0.6483 (mmt180) REVERT: A 232 PHE cc_start: 0.7901 (OUTLIER) cc_final: 0.7527 (t80) REVERT: A 248 ASP cc_start: 0.8169 (m-30) cc_final: 0.7705 (t70) REVERT: B 78 ARG cc_start: 0.7752 (mmt180) cc_final: 0.6805 (mmm160) REVERT: D 29 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8458 (pp) outliers start: 16 outliers final: 12 residues processed: 75 average time/residue: 0.2111 time to fit residues: 18.7829 Evaluate side-chains 78 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 63 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain D residue 2 GLN Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain G residue 11 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 6 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 26 optimal weight: 0.0070 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 1 optimal weight: 0.0870 chunk 29 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.143528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.118046 restraints weight = 5188.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.121527 restraints weight = 3203.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.123831 restraints weight = 2351.716| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3364 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3348 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 3854 Z= 0.202 Angle : 0.523 6.756 5235 Z= 0.272 Chirality : 0.043 0.142 604 Planarity : 0.003 0.030 652 Dihedral : 4.783 30.712 530 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.61 % Allowed : 22.89 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % 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: -2.48 (0.39), residues: 474 helix: -2.37 (0.52), residues: 91 sheet: -0.56 (0.45), residues: 149 loop : -2.06 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 33 HIS 0.002 0.001 HIS A 26 PHE 0.011 0.001 PHE A 177 TYR 0.011 0.001 TYR A 213 ARG 0.002 0.000 ARG D 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1454.19 seconds wall clock time: 27 minutes 41.56 seconds (1661.56 seconds total)