Starting phenix.real_space_refine on Sun Mar 10 15:58:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esb_28574/03_2024/8esb_28574.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esb_28574/03_2024/8esb_28574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esb_28574/03_2024/8esb_28574.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esb_28574/03_2024/8esb_28574.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esb_28574/03_2024/8esb_28574.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esb_28574/03_2024/8esb_28574.pdb" } resolution = 3.12 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 66 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 1970 2.51 5 N 563 2.21 5 O 593 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 106": "OD1" <-> "OD2" Residue "A TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 173": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3140 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2223 Classifications: {'peptide': 273} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 260} Chain breaks: 1 Chain: "B" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 828 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 93} Chain: "C" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 89 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Time building chain proxies: 2.18, per 1000 atoms: 0.69 Number of scatterers: 3140 At special positions: 0 Unit cell: (84.15, 62.05, 66.3, 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 593 8.00 N 563 7.00 C 1970 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS C 12 " distance=2.03 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 259 " distance=2.03 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 80 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 0.94 Conformation dependent library (CDL) restraints added in 514.0 milliseconds 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 716 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 7 sheets defined 20.6% alpha, 41.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 49 through 53 removed outlier: 3.668A pdb=" N ILE A 52 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU A 53 " --> pdb=" O PRO A 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 49 through 53' Processing helix chain 'A' and resid 56 through 84 removed outlier: 3.763A pdb=" N TRP A 60 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A 71 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR A 73 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL A 76 " --> pdb=" O GLN A 72 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 149 Processing helix chain 'A' and resid 151 through 162 removed outlier: 3.636A pdb=" N ALA A 158 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TYR A 159 " --> pdb=" O GLN A 155 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 Processing helix chain 'A' and resid 175 through 180 removed outlier: 3.513A pdb=" N GLN A 180 " --> pdb=" O LYS A 176 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 47 removed outlier: 6.836A pdb=" N GLY A 26 " --> pdb=" O PHE A 33 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ARG A 35 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA A 24 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASP A 37 " --> pdb=" O PHE A 22 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N PHE A 22 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN A 96 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET A 98 " --> pdb=" O GLN A 115 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR A 113 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG A 111 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N HIS A 114 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ALA A 125 " --> pdb=" O HIS A 114 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N TYR A 116 " --> pdb=" O TYR A 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 191 removed outlier: 3.543A pdb=" N HIS A 188 " --> pdb=" O TRP A 204 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG A 202 " --> pdb=" O THR A 190 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 201 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N PHE A 241 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 186 through 191 removed outlier: 3.543A pdb=" N HIS A 188 " --> pdb=" O TRP A 204 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG A 202 " --> pdb=" O THR A 190 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 201 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N PHE A 241 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 223 removed outlier: 3.790A pdb=" N GLU A 222 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 214 " --> pdb=" O GLN A 262 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 6 through 11 Processing sheet with id=AA6, first strand: chain 'B' and resid 6 through 11 removed outlier: 5.737A pdb=" N PHE B 62 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER B 55 " --> pdb=" O TYR B 63 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 44 through 45 146 hydrogen bonds defined for protein. 384 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: 0.82 Time building geometry restraints manager: 1.06 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: 1050 1.34 - 1.46: 765 1.46 - 1.58: 1393 1.58 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 3228 Sorted by residual: bond pdb=" CB ARG B 45 " pdb=" CG ARG B 45 " ideal model delta sigma weight residual 1.520 1.483 0.037 3.00e-02 1.11e+03 1.50e+00 bond pdb=" CB PRO B 32 " pdb=" CG PRO B 32 " ideal model delta sigma weight residual 1.506 1.461 0.045 3.90e-02 6.57e+02 1.35e+00 bond pdb=" CG1 ILE B 92 " pdb=" CD1 ILE B 92 " ideal model delta sigma weight residual 1.513 1.469 0.044 3.90e-02 6.57e+02 1.28e+00 bond pdb=" CB PRO A 210 " pdb=" CG PRO A 210 " ideal model delta sigma weight residual 1.506 1.463 0.043 3.90e-02 6.57e+02 1.20e+00 bond pdb=" CB THR A 143 " pdb=" CG2 THR A 143 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.37e-01 ... (remaining 3223 not shown) Histogram of bond angle deviations from ideal: 100.41 - 107.14: 118 107.14 - 113.87: 1719 113.87 - 120.60: 1262 120.60 - 127.33: 1217 127.33 - 134.07: 58 Bond angle restraints: 4374 Sorted by residual: angle pdb=" N VAL A 28 " pdb=" CA VAL A 28 " pdb=" C VAL A 28 " ideal model delta sigma weight residual 109.34 102.32 7.02 2.08e+00 2.31e-01 1.14e+01 angle pdb=" CA LEU A 156 " pdb=" CB LEU A 156 " pdb=" CG LEU A 156 " ideal model delta sigma weight residual 116.30 127.98 -11.68 3.50e+00 8.16e-02 1.11e+01 angle pdb=" N ASP A 29 " pdb=" CA ASP A 29 " pdb=" C ASP A 29 " ideal model delta sigma weight residual 110.80 115.73 -4.93 2.13e+00 2.20e-01 5.36e+00 angle pdb=" CB ARG B 45 " pdb=" CG ARG B 45 " pdb=" CD ARG B 45 " ideal model delta sigma weight residual 111.30 106.68 4.62 2.30e+00 1.89e-01 4.03e+00 angle pdb=" C ALA A 150 " pdb=" N HIS A 151 " pdb=" CA HIS A 151 " ideal model delta sigma weight residual 121.54 125.03 -3.49 1.91e+00 2.74e-01 3.33e+00 ... (remaining 4369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 1688 16.43 - 32.86: 167 32.86 - 49.28: 35 49.28 - 65.71: 9 65.71 - 82.14: 6 Dihedral angle restraints: 1905 sinusoidal: 789 harmonic: 1116 Sorted by residual: dihedral pdb=" CA TYR A 27 " pdb=" C TYR A 27 " pdb=" N VAL A 28 " pdb=" CA VAL A 28 " ideal model delta harmonic sigma weight residual 180.00 150.93 29.07 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA VAL A 28 " pdb=" C VAL A 28 " pdb=" N ASP A 29 " pdb=" CA ASP A 29 " ideal model delta harmonic sigma weight residual -180.00 -160.71 -19.29 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA GLY A 162 " pdb=" C GLY A 162 " pdb=" N THR A 163 " pdb=" CA THR A 163 " ideal model delta harmonic sigma weight residual 180.00 -161.60 -18.40 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 1902 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 231 0.032 - 0.063: 147 0.063 - 0.095: 45 0.095 - 0.126: 13 0.126 - 0.158: 7 Chirality restraints: 443 Sorted by residual: chirality pdb=" CA VAL A 28 " pdb=" N VAL A 28 " pdb=" C VAL A 28 " pdb=" CB VAL A 28 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" CA VAL A 34 " pdb=" N VAL A 34 " pdb=" C VAL A 34 " pdb=" CB VAL A 34 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA ILE B 92 " pdb=" N ILE B 92 " pdb=" C ILE B 92 " pdb=" CB ILE B 92 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 ... (remaining 440 not shown) Planarity restraints: 571 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 274 " -0.011 2.00e-02 2.50e+03 7.29e-03 1.33e+00 pdb=" CG TRP A 274 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP A 274 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A 274 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 274 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 274 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 274 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 274 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 274 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 274 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 111 " -0.093 9.50e-02 1.11e+02 4.17e-02 1.30e+00 pdb=" NE ARG A 111 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG A 111 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 111 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 111 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 159 " -0.005 2.00e-02 2.50e+03 1.09e-02 1.19e+00 pdb=" C TYR A 159 " 0.019 2.00e-02 2.50e+03 pdb=" O TYR A 159 " -0.007 2.00e-02 2.50e+03 pdb=" N LEU A 160 " -0.006 2.00e-02 2.50e+03 ... (remaining 568 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 625 2.78 - 3.31: 2582 3.31 - 3.84: 4605 3.84 - 4.37: 5599 4.37 - 4.90: 10192 Nonbonded interactions: 23603 Sorted by model distance: nonbonded pdb=" OD2 ASP A 77 " pdb=" OH TYR A 116 " model vdw 2.245 2.440 nonbonded pdb=" OD1 ASP A 122 " pdb=" NE1 TRP B 60 " model vdw 2.285 2.520 nonbonded pdb=" O TRP A 107 " pdb=" NH1 ARG A 169 " model vdw 2.332 2.520 nonbonded pdb=" NH2 ARG A 14 " pdb=" O GLU A 19 " model vdw 2.364 2.520 nonbonded pdb=" O SER A 207 " pdb=" OG SER A 207 " model vdw 2.368 2.440 ... (remaining 23598 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 9.400 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.780 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 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 0.045 3228 Z= 0.372 Angle : 0.626 11.683 4374 Z= 0.331 Chirality : 0.046 0.158 443 Planarity : 0.004 0.042 571 Dihedral : 14.313 82.140 1177 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -2.63 (0.41), residues: 376 helix: -0.87 (0.61), residues: 75 sheet: -1.36 (0.44), residues: 135 loop : -2.43 (0.42), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 274 HIS 0.004 0.001 HIS A 114 PHE 0.010 0.002 PHE A 33 TYR 0.016 0.001 TYR A 99 ARG 0.009 0.001 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.371 Fit side-chains REVERT: A 98 MET cc_start: 0.7866 (tmm) cc_final: 0.7622 (tmm) REVERT: A 269 PRO cc_start: 0.8741 (Cg_exo) cc_final: 0.8416 (Cg_endo) REVERT: B 19 LYS cc_start: 0.8723 (mmtm) cc_final: 0.8482 (mptt) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.2292 time to fit residues: 11.7670 Evaluate side-chains 41 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3228 Z= 0.268 Angle : 0.557 7.439 4374 Z= 0.297 Chirality : 0.044 0.162 443 Planarity : 0.004 0.026 571 Dihedral : 4.619 28.277 429 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.30 % Allowed : 6.63 % Favored : 93.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.42), residues: 376 helix: -0.27 (0.62), residues: 75 sheet: -0.42 (0.44), residues: 134 loop : -2.18 (0.43), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 274 HIS 0.006 0.001 HIS C 8 PHE 0.009 0.002 PHE A 33 TYR 0.015 0.001 TYR A 99 ARG 0.004 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.390 Fit side-chains REVERT: A 269 PRO cc_start: 0.8913 (Cg_exo) cc_final: 0.8680 (Cg_endo) REVERT: B 19 LYS cc_start: 0.8689 (mmtm) cc_final: 0.8464 (mptt) outliers start: 1 outliers final: 0 residues processed: 39 average time/residue: 0.2268 time to fit residues: 10.4606 Evaluate side-chains 37 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 18 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 0.0030 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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: 0.8257 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3228 Z= 0.192 Angle : 0.489 7.236 4374 Z= 0.261 Chirality : 0.042 0.161 443 Planarity : 0.003 0.030 571 Dihedral : 4.360 27.642 429 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.51 % Allowed : 9.64 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -0.90 (0.43), residues: 376 helix: 0.82 (0.64), residues: 69 sheet: 0.23 (0.45), residues: 134 loop : -1.91 (0.45), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 204 HIS 0.003 0.001 HIS C 8 PHE 0.008 0.001 PHE A 33 TYR 0.015 0.001 TYR A 99 ARG 0.004 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 0.374 Fit side-chains REVERT: A 269 PRO cc_start: 0.8923 (Cg_exo) cc_final: 0.8711 (Cg_endo) REVERT: B 19 LYS cc_start: 0.8674 (mmtm) cc_final: 0.8459 (mptt) outliers start: 5 outliers final: 2 residues processed: 44 average time/residue: 0.2160 time to fit residues: 11.1963 Evaluate side-chains 42 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain B residue 88 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.8256 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3228 Z= 0.203 Angle : 0.503 9.528 4374 Z= 0.260 Chirality : 0.042 0.153 443 Planarity : 0.003 0.033 571 Dihedral : 4.266 27.501 429 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.11 % Allowed : 9.64 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -0.47 (0.44), residues: 376 helix: 1.20 (0.65), residues: 69 sheet: 0.37 (0.46), residues: 139 loop : -1.57 (0.47), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 204 HIS 0.002 0.001 HIS A 114 PHE 0.009 0.001 PHE A 33 TYR 0.016 0.001 TYR A 99 ARG 0.003 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 0.372 Fit side-chains REVERT: A 269 PRO cc_start: 0.8898 (Cg_exo) cc_final: 0.8696 (Cg_endo) REVERT: B 19 LYS cc_start: 0.8669 (mmtm) cc_final: 0.8455 (mptt) outliers start: 7 outliers final: 5 residues processed: 44 average time/residue: 0.2273 time to fit residues: 11.7052 Evaluate side-chains 45 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 40 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain C residue 8 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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: 0.8278 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3228 Z= 0.270 Angle : 0.510 7.434 4374 Z= 0.268 Chirality : 0.043 0.143 443 Planarity : 0.003 0.036 571 Dihedral : 4.353 28.075 429 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.51 % Allowed : 12.35 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -0.27 (0.45), residues: 376 helix: 1.30 (0.64), residues: 69 sheet: 0.57 (0.46), residues: 139 loop : -1.50 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 167 HIS 0.003 0.001 HIS A 114 PHE 0.009 0.002 PHE B 30 TYR 0.018 0.001 TYR A 99 ARG 0.002 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.385 Fit side-chains REVERT: B 19 LYS cc_start: 0.8696 (mmtm) cc_final: 0.8476 (mptt) outliers start: 5 outliers final: 5 residues processed: 41 average time/residue: 0.2244 time to fit residues: 10.8112 Evaluate side-chains 44 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain C residue 8 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8276 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3228 Z= 0.256 Angle : 0.500 7.441 4374 Z= 0.263 Chirality : 0.043 0.142 443 Planarity : 0.003 0.027 571 Dihedral : 4.308 28.042 429 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.81 % Allowed : 12.35 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -0.14 (0.45), residues: 376 helix: 1.35 (0.64), residues: 69 sheet: 0.69 (0.46), residues: 139 loop : -1.43 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 167 HIS 0.003 0.001 HIS A 114 PHE 0.009 0.001 PHE B 30 TYR 0.018 0.001 TYR A 99 ARG 0.002 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.378 Fit side-chains REVERT: B 19 LYS cc_start: 0.8704 (mmtm) cc_final: 0.8501 (mptt) outliers start: 6 outliers final: 4 residues processed: 43 average time/residue: 0.2343 time to fit residues: 11.7515 Evaluate side-chains 43 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 88 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.8270 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3228 Z= 0.235 Angle : 0.489 7.370 4374 Z= 0.258 Chirality : 0.042 0.143 443 Planarity : 0.003 0.027 571 Dihedral : 4.246 27.914 429 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.11 % Allowed : 12.35 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -0.09 (0.44), residues: 376 helix: 1.46 (0.64), residues: 69 sheet: 1.04 (0.46), residues: 129 loop : -1.60 (0.46), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 167 HIS 0.003 0.001 HIS C 8 PHE 0.008 0.001 PHE B 30 TYR 0.017 0.001 TYR A 99 ARG 0.002 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.353 Fit side-chains REVERT: A 106 ASP cc_start: 0.8103 (p0) cc_final: 0.7445 (p0) REVERT: A 108 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7430 (mtm-85) REVERT: B 19 LYS cc_start: 0.8694 (mmtm) cc_final: 0.8488 (mptt) outliers start: 7 outliers final: 5 residues processed: 43 average time/residue: 0.2049 time to fit residues: 10.4106 Evaluate side-chains 46 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain B residue 73 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 22 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 3 optimal weight: 0.8980 chunk 28 optimal weight: 0.0670 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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: 0.8248 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3228 Z= 0.177 Angle : 0.467 7.034 4374 Z= 0.247 Chirality : 0.042 0.158 443 Planarity : 0.003 0.028 571 Dihedral : 4.072 27.348 429 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.41 % Allowed : 12.05 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 0.04 (0.45), residues: 376 helix: 1.61 (0.64), residues: 69 sheet: 1.10 (0.46), residues: 129 loop : -1.53 (0.47), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 204 HIS 0.003 0.001 HIS C 8 PHE 0.008 0.001 PHE A 33 TYR 0.015 0.001 TYR A 99 ARG 0.002 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 39 time to evaluate : 0.400 Fit side-chains REVERT: A 106 ASP cc_start: 0.8082 (p0) cc_final: 0.7418 (p0) REVERT: A 108 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7404 (mtm-85) REVERT: B 19 LYS cc_start: 0.8657 (mmtm) cc_final: 0.8448 (mptt) outliers start: 8 outliers final: 6 residues processed: 43 average time/residue: 0.2255 time to fit residues: 11.6314 Evaluate side-chains 46 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain B residue 73 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 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: 0.8265 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3228 Z= 0.226 Angle : 0.483 7.264 4374 Z= 0.256 Chirality : 0.042 0.143 443 Planarity : 0.003 0.027 571 Dihedral : 4.173 27.748 429 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.01 % Allowed : 11.45 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 0.06 (0.44), residues: 376 helix: 1.65 (0.63), residues: 69 sheet: 1.18 (0.46), residues: 128 loop : -1.56 (0.47), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 244 HIS 0.004 0.001 HIS C 8 PHE 0.008 0.001 PHE A 33 TYR 0.017 0.001 TYR A 99 ARG 0.002 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 40 time to evaluate : 0.368 Fit side-chains REVERT: A 106 ASP cc_start: 0.8120 (p0) cc_final: 0.7486 (p0) REVERT: A 108 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7417 (mtm-85) REVERT: B 19 LYS cc_start: 0.8677 (mmtm) cc_final: 0.8460 (mptt) outliers start: 10 outliers final: 7 residues processed: 45 average time/residue: 0.2100 time to fit residues: 11.1124 Evaluate side-chains 49 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 41 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 88 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 23 optimal weight: 0.2980 chunk 31 optimal weight: 0.9980 chunk 8 optimal weight: 0.1980 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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: 0.8240 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3228 Z= 0.168 Angle : 0.483 8.858 4374 Z= 0.249 Chirality : 0.042 0.150 443 Planarity : 0.003 0.028 571 Dihedral : 4.019 27.294 429 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.11 % Allowed : 12.05 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 0.20 (0.45), residues: 376 helix: 1.88 (0.64), residues: 69 sheet: 1.21 (0.46), residues: 129 loop : -1.50 (0.47), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 204 HIS 0.003 0.001 HIS C 8 PHE 0.008 0.001 PHE A 33 TYR 0.014 0.001 TYR A 99 ARG 0.002 0.000 ARG A 108 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.370 Fit side-chains REVERT: A 106 ASP cc_start: 0.8096 (p0) cc_final: 0.7451 (p0) REVERT: A 108 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7399 (mtm-85) REVERT: B 19 LYS cc_start: 0.8637 (mmtm) cc_final: 0.8425 (mptt) outliers start: 7 outliers final: 6 residues processed: 43 average time/residue: 0.1877 time to fit residues: 9.6022 Evaluate side-chains 47 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 88 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3647 r_free = 0.3647 target = 0.124989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.088912 restraints weight = 4286.173| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 3.21 r_work: 0.2955 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3228 Z= 0.235 Angle : 0.502 8.474 4374 Z= 0.260 Chirality : 0.042 0.141 443 Planarity : 0.003 0.028 571 Dihedral : 4.151 27.725 429 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.41 % Allowed : 12.05 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 0.14 (0.45), residues: 376 helix: 1.80 (0.64), residues: 69 sheet: 1.20 (0.46), residues: 129 loop : -1.53 (0.47), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 244 HIS 0.005 0.001 HIS C 8 PHE 0.008 0.001 PHE B 30 TYR 0.017 0.001 TYR A 99 ARG 0.002 0.000 ARG A 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1175.99 seconds wall clock time: 21 minutes 54.44 seconds (1314.44 seconds total)