Starting phenix.real_space_refine on Mon Jun 24 17:28:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w22_43737/06_2024/8w22_43737.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w22_43737/06_2024/8w22_43737.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w22_43737/06_2024/8w22_43737.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w22_43737/06_2024/8w22_43737.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w22_43737/06_2024/8w22_43737.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w22_43737/06_2024/8w22_43737.pdb" } resolution = 4.0 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= 0.072 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 13 5.16 5 C 2333 2.51 5 N 723 2.21 5 O 681 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 3750 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 685 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 3, 'TRANS': 95} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 53 Chain: "B" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 805 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 117} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 4, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 65 Chain: "C" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 2260 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 242} Link IDs: {'PTRANS': 17, 'TRANS': 387} Chain breaks: 12 Unresolved non-hydrogen bonds: 798 Unresolved non-hydrogen angles: 1047 Unresolved non-hydrogen dihedrals: 629 Unresolved non-hydrogen chiralities: 100 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 37, 'TYR:plan': 7, 'ASN:plan1': 18, 'TRP:plan': 7, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 428 Time building chain proxies: 3.27, per 1000 atoms: 0.87 Number of scatterers: 3750 At special positions: 0 Unit cell: (69.126, 131.508, 116.334, 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 13 16.00 O 681 8.00 N 723 7.00 C 2333 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 78 " - pdb=" SG CYS B 96 " distance=2.05 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 71 " distance=2.08 Simple disulfide: pdb=" SG CYS C 192 " - pdb=" SG CYS C 222 " 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: 1.26 Conformation dependent library (CDL) restraints added in 812.1 milliseconds 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1122 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 9 sheets defined 19.4% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 99 through 111 removed outlier: 3.577A pdb=" N MET A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 123 removed outlier: 3.959A pdb=" N ASP A 121 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 134 Processing helix chain 'A' and resid 136 through 139 Processing helix chain 'A' and resid 140 through 145 Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 158 through 170 Processing helix chain 'A' and resid 172 through 180 Processing helix chain 'A' and resid 182 through 197 Processing helix chain 'B' and resid 54 through 62 removed outlier: 3.504A pdb=" N ALA B 60 " --> pdb=" O ALA B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 151 Processing helix chain 'C' and resid 69 through 73 Processing helix chain 'C' and resid 238 through 247 Processing sheet with id=AA1, first strand: chain 'B' and resid 73 through 76 removed outlier: 3.711A pdb=" N CYS B 96 " --> pdb=" O THR B 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 104 through 106 removed outlier: 3.525A pdb=" N ALA B 104 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR B 126 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LEU B 162 " --> pdb=" O LYS B 124 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LYS B 124 " --> pdb=" O LEU B 162 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 43 through 48 removed outlier: 3.536A pdb=" N GLU C 112 " --> pdb=" O ARG C 125 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N THR C 91 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 137 through 138 removed outlier: 7.338A pdb=" N ARG C 137 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N GLY C 212 " --> pdb=" O ARG C 137 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE C 233 " --> pdb=" O ASN C 215 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N SER C 217 " --> pdb=" O ASP C 231 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ASP C 231 " --> pdb=" O SER C 217 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N THR C 184 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N VAL C 173 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASP C 203 " --> pdb=" O PRO C 148 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL C 152 " --> pdb=" O PRO C 199 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY C 212 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLN C 202 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU C 210 " --> pdb=" O GLN C 202 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LYS C 204 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LEU C 208 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 259 through 262 Processing sheet with id=AA6, first strand: chain 'C' and resid 333 through 334 Processing sheet with id=AA7, first strand: chain 'C' and resid 369 through 369 Processing sheet with id=AA8, first strand: chain 'C' and resid 409 through 413 removed outlier: 3.529A pdb=" N THR C 411 " --> pdb=" O THR C 425 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N THR C 425 " --> pdb=" O THR C 411 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 485 through 486 173 hydrogen bonds defined for protein. 453 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: 1.18 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1142 1.33 - 1.45: 504 1.45 - 1.58: 2130 1.58 - 1.70: 0 1.70 - 1.82: 20 Bond restraints: 3796 Sorted by residual: bond pdb=" NE ARG A 106 " pdb=" CZ ARG A 106 " ideal model delta sigma weight residual 1.326 1.355 -0.029 1.10e-02 8.26e+03 6.76e+00 bond pdb=" NE ARG C 119 " pdb=" CZ ARG C 119 " ideal model delta sigma weight residual 1.326 1.353 -0.027 1.10e-02 8.26e+03 6.04e+00 bond pdb=" NE ARG A 162 " pdb=" CZ ARG A 162 " ideal model delta sigma weight residual 1.326 1.351 -0.025 1.10e-02 8.26e+03 5.31e+00 bond pdb=" NE ARG C 97 " pdb=" CZ ARG C 97 " ideal model delta sigma weight residual 1.326 1.351 -0.025 1.10e-02 8.26e+03 5.20e+00 bond pdb=" NE ARG A 124 " pdb=" CZ ARG A 124 " ideal model delta sigma weight residual 1.326 1.351 -0.025 1.10e-02 8.26e+03 5.05e+00 ... (remaining 3791 not shown) Histogram of bond angle deviations from ideal: 100.71 - 107.29: 133 107.29 - 113.87: 2023 113.87 - 120.45: 1219 120.45 - 127.03: 1800 127.03 - 133.61: 20 Bond angle restraints: 5195 Sorted by residual: angle pdb=" C VAL C 114 " pdb=" N PRO C 115 " pdb=" CA PRO C 115 " ideal model delta sigma weight residual 119.85 127.71 -7.86 1.01e+00 9.80e-01 6.05e+01 angle pdb=" C ASP B 121 " pdb=" N PRO B 122 " pdb=" CA PRO B 122 " ideal model delta sigma weight residual 119.76 126.92 -7.16 1.03e+00 9.43e-01 4.84e+01 angle pdb=" C ARG C 502 " pdb=" N PRO C 503 " pdb=" CA PRO C 503 " ideal model delta sigma weight residual 120.03 126.91 -6.88 9.90e-01 1.02e+00 4.83e+01 angle pdb=" C GLY A 158 " pdb=" N PRO A 159 " pdb=" CA PRO A 159 " ideal model delta sigma weight residual 119.32 127.23 -7.91 1.14e+00 7.69e-01 4.81e+01 angle pdb=" C MET B 43 " pdb=" N PRO B 44 " pdb=" CA PRO B 44 " ideal model delta sigma weight residual 120.31 127.11 -6.80 9.80e-01 1.04e+00 4.81e+01 ... (remaining 5190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.31: 2128 12.31 - 24.61: 57 24.61 - 36.92: 16 36.92 - 49.23: 6 49.23 - 61.53: 6 Dihedral angle restraints: 2213 sinusoidal: 467 harmonic: 1746 Sorted by residual: dihedral pdb=" CB CYS C 192 " pdb=" SG CYS C 192 " pdb=" SG CYS C 222 " pdb=" CB CYS C 222 " ideal model delta sinusoidal sigma weight residual 93.00 154.53 -61.53 1 1.00e+01 1.00e-02 5.02e+01 dihedral pdb=" CB CYS C 55 " pdb=" SG CYS C 55 " pdb=" SG CYS C 71 " pdb=" CB CYS C 71 " ideal model delta sinusoidal sigma weight residual 93.00 137.06 -44.06 1 1.00e+01 1.00e-02 2.70e+01 dihedral pdb=" CB CYS B 78 " pdb=" SG CYS B 78 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 120.80 -27.80 1 1.00e+01 1.00e-02 1.11e+01 ... (remaining 2210 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 349 0.039 - 0.079: 170 0.079 - 0.118: 73 0.118 - 0.157: 24 0.157 - 0.197: 3 Chirality restraints: 619 Sorted by residual: chirality pdb=" CA ILE C 191 " pdb=" N ILE C 191 " pdb=" C ILE C 191 " pdb=" CB ILE C 191 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.66e-01 chirality pdb=" CA ILE C 130 " pdb=" N ILE C 130 " pdb=" C ILE C 130 " pdb=" CB ILE C 130 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.54e-01 chirality pdb=" CG LEU C 46 " pdb=" CB LEU C 46 " pdb=" CD1 LEU C 46 " pdb=" CD2 LEU C 46 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.70e-01 ... (remaining 616 not shown) Planarity restraints: 718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 52 " -0.028 2.00e-02 2.50e+03 1.43e-02 4.08e+00 pdb=" CG TYR B 52 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR B 52 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR B 52 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR B 52 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 52 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 52 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 52 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 199 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.34e+00 pdb=" C PRO C 199 " 0.032 2.00e-02 2.50e+03 pdb=" O PRO C 199 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU C 200 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 52 " 0.021 2.00e-02 2.50e+03 1.11e-02 2.48e+00 pdb=" CG TYR C 52 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR C 52 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR C 52 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR C 52 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR C 52 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 52 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 52 " 0.015 2.00e-02 2.50e+03 ... (remaining 715 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 1763 2.98 - 3.46: 3227 3.46 - 3.94: 5318 3.94 - 4.42: 5604 4.42 - 4.90: 9568 Nonbonded interactions: 25480 Sorted by model distance: nonbonded pdb=" O TYR B 147 " pdb=" C GLY B 148 " model vdw 2.497 3.270 nonbonded pdb=" O TYR B 147 " pdb=" N ALA B 150 " model vdw 2.511 2.520 nonbonded pdb=" N GLY C 194 " pdb=" N ASP C 195 " model vdw 2.565 2.560 nonbonded pdb=" N LYS C 39 " pdb=" N LEU C 40 " model vdw 2.578 2.560 nonbonded pdb=" N GLY C 268 " pdb=" N ARG C 269 " model vdw 2.602 2.560 ... (remaining 25475 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 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.890 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.440 Find NCS groups from input model: 0.120 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 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 : 0.008 0.050 3796 Z= 0.572 Angle : 1.266 7.910 5195 Z= 0.882 Chirality : 0.055 0.197 619 Planarity : 0.005 0.018 718 Dihedral : 7.997 59.354 1082 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 0.92 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.84 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.30 (0.35), residues: 599 helix: -0.58 (0.43), residues: 110 sheet: 1.43 (0.46), residues: 140 loop : 0.03 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.004 TRP C 64 HIS 0.004 0.001 HIS C 116 PHE 0.018 0.003 PHE C 171 TYR 0.028 0.004 TYR B 52 ARG 0.004 0.000 ARG C 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.379 Fit side-chains REVERT: A 106 ARG cc_start: 0.6014 (ttm110) cc_final: 0.5118 (tpp-160) REVERT: A 170 GLN cc_start: 0.8282 (mt0) cc_final: 0.8030 (mt0) REVERT: B 100 MET cc_start: 0.8401 (mmm) cc_final: 0.7447 (mpp) REVERT: C 125 ARG cc_start: 0.7762 (ttt180) cc_final: 0.7217 (tmt-80) REVERT: C 137 ARG cc_start: 0.7417 (mtp180) cc_final: 0.7137 (mtp85) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1956 time to fit residues: 16.7226 Evaluate side-chains 41 residues out of total 489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 55 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3796 Z= 0.311 Angle : 0.625 5.424 5195 Z= 0.342 Chirality : 0.047 0.183 619 Planarity : 0.005 0.028 718 Dihedral : 4.376 19.023 644 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.89 % Allowed : 13.89 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.76 (0.36), residues: 599 helix: 0.81 (0.49), residues: 115 sheet: 0.97 (0.43), residues: 165 loop : 0.25 (0.38), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 117 HIS 0.003 0.001 HIS C 116 PHE 0.017 0.003 PHE C 171 TYR 0.018 0.002 TYR C 52 ARG 0.005 0.001 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.406 Fit side-chains REVERT: A 106 ARG cc_start: 0.5670 (ttm110) cc_final: 0.4943 (tpp-160) REVERT: A 156 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8507 (tt) REVERT: B 100 MET cc_start: 0.9077 (mmm) cc_final: 0.8759 (mmt) REVERT: C 137 ARG cc_start: 0.7811 (mtp180) cc_final: 0.7368 (mtp85) outliers start: 7 outliers final: 4 residues processed: 48 average time/residue: 0.1310 time to fit residues: 8.2676 Evaluate side-chains 45 residues out of total 489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 40 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 137 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 0.0980 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 55 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 18 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 3796 Z= 0.366 Angle : 0.648 6.756 5195 Z= 0.350 Chirality : 0.048 0.159 619 Planarity : 0.005 0.033 718 Dihedral : 4.671 19.435 644 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 5.56 % Allowed : 17.78 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.19 (0.36), residues: 599 helix: 0.77 (0.53), residues: 109 sheet: 0.55 (0.43), residues: 162 loop : -0.24 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 117 HIS 0.006 0.002 HIS B 72 PHE 0.015 0.003 PHE C 171 TYR 0.016 0.002 TYR A 185 ARG 0.002 0.000 ARG C 125 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 41 time to evaluate : 0.409 Fit side-chains REVERT: B 100 MET cc_start: 0.8923 (mmm) cc_final: 0.8659 (mmm) REVERT: C 59 LEU cc_start: 0.7745 (mp) cc_final: 0.7525 (mp) REVERT: C 137 ARG cc_start: 0.8220 (mtp180) cc_final: 0.7615 (mtp85) outliers start: 10 outliers final: 6 residues processed: 47 average time/residue: 0.1168 time to fit residues: 7.3931 Evaluate side-chains 43 residues out of total 489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 164 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 26 optimal weight: 0.0670 chunk 37 optimal weight: 0.7980 chunk 55 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 52 optimal weight: 20.0000 chunk 15 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN C 167 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3796 Z= 0.228 Angle : 0.529 5.533 5195 Z= 0.281 Chirality : 0.045 0.145 619 Planarity : 0.004 0.034 718 Dihedral : 3.990 15.300 644 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 5.56 % Allowed : 18.89 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.32 (0.37), residues: 599 helix: 1.07 (0.54), residues: 109 sheet: 0.51 (0.43), residues: 162 loop : -0.16 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 117 HIS 0.004 0.001 HIS B 72 PHE 0.015 0.002 PHE C 171 TYR 0.007 0.001 TYR A 185 ARG 0.002 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 37 time to evaluate : 0.399 Fit side-chains REVERT: B 100 MET cc_start: 0.9048 (mmm) cc_final: 0.8759 (mmm) REVERT: C 137 ARG cc_start: 0.8211 (mtp180) cc_final: 0.7561 (mtp85) REVERT: C 264 PHE cc_start: 0.5782 (m-80) cc_final: 0.5552 (m-80) outliers start: 10 outliers final: 7 residues processed: 46 average time/residue: 0.1232 time to fit residues: 7.6521 Evaluate side-chains 44 residues out of total 489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 37 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 164 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 14 optimal weight: 0.0870 chunk 19 optimal weight: 0.6980 chunk 53 optimal weight: 20.0000 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3796 Z= 0.332 Angle : 0.603 6.330 5195 Z= 0.323 Chirality : 0.047 0.153 619 Planarity : 0.004 0.034 718 Dihedral : 4.392 17.799 644 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 6.11 % Allowed : 18.33 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 (0.37), residues: 599 helix: 0.86 (0.55), residues: 108 sheet: 0.56 (0.46), residues: 142 loop : -0.30 (0.36), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 117 HIS 0.004 0.002 HIS B 72 PHE 0.015 0.003 PHE B 97 TYR 0.010 0.001 TYR A 185 ARG 0.002 0.001 ARG C 125 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 38 time to evaluate : 0.373 Fit side-chains REVERT: B 100 MET cc_start: 0.8950 (mmm) cc_final: 0.8739 (mmm) REVERT: C 125 ARG cc_start: 0.7843 (ttt90) cc_final: 0.7218 (tmm-80) REVERT: C 137 ARG cc_start: 0.8379 (mtp180) cc_final: 0.7638 (mtp85) REVERT: C 264 PHE cc_start: 0.5579 (m-80) cc_final: 0.5336 (m-80) outliers start: 11 outliers final: 9 residues processed: 47 average time/residue: 0.1236 time to fit residues: 7.8543 Evaluate side-chains 46 residues out of total 489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 37 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 164 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.0970 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 6 optimal weight: 0.4980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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: 0.7680 moved from start: 0.5256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3796 Z= 0.226 Angle : 0.542 7.423 5195 Z= 0.279 Chirality : 0.045 0.135 619 Planarity : 0.004 0.035 718 Dihedral : 3.911 15.621 644 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 6.11 % Allowed : 20.00 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.18 (0.37), residues: 599 helix: 1.01 (0.55), residues: 109 sheet: 0.31 (0.45), residues: 143 loop : -0.19 (0.36), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 117 HIS 0.004 0.001 HIS B 72 PHE 0.016 0.002 PHE B 144 TYR 0.006 0.001 TYR A 138 ARG 0.003 0.000 ARG C 125 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 38 time to evaluate : 0.378 Fit side-chains REVERT: C 125 ARG cc_start: 0.8207 (ttt90) cc_final: 0.7611 (tmm-80) REVERT: C 137 ARG cc_start: 0.8373 (mtp180) cc_final: 0.7617 (mtp85) REVERT: C 264 PHE cc_start: 0.5454 (m-80) cc_final: 0.5208 (m-80) outliers start: 11 outliers final: 9 residues processed: 47 average time/residue: 0.1152 time to fit residues: 7.3805 Evaluate side-chains 44 residues out of total 489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 35 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 164 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 32 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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: 0.7771 moved from start: 0.5691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 3796 Z= 0.424 Angle : 0.672 8.190 5195 Z= 0.357 Chirality : 0.049 0.186 619 Planarity : 0.005 0.036 718 Dihedral : 4.765 20.595 644 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 8.33 % Allowed : 18.89 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.30 (0.36), residues: 599 helix: 0.25 (0.53), residues: 112 sheet: 0.08 (0.44), residues: 143 loop : -0.40 (0.36), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 117 HIS 0.006 0.002 HIS B 72 PHE 0.023 0.003 PHE B 97 TYR 0.009 0.002 TYR B 52 ARG 0.003 0.001 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 34 time to evaluate : 0.371 Fit side-chains REVERT: C 125 ARG cc_start: 0.8290 (ttt90) cc_final: 0.7671 (tmm-80) REVERT: C 137 ARG cc_start: 0.8480 (mtp180) cc_final: 0.7696 (mtp85) REVERT: C 264 PHE cc_start: 0.5320 (m-80) cc_final: 0.5056 (m-80) outliers start: 15 outliers final: 14 residues processed: 45 average time/residue: 0.1254 time to fit residues: 7.7444 Evaluate side-chains 47 residues out of total 489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 33 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 164 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 chunk 54 optimal weight: 0.0050 chunk 32 optimal weight: 0.8980 overall best weight: 0.6796 ------------------------------------------------------------------------------- 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: 0.7711 moved from start: 0.5722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3796 Z= 0.249 Angle : 0.569 9.684 5195 Z= 0.293 Chirality : 0.046 0.136 619 Planarity : 0.004 0.037 718 Dihedral : 4.133 16.784 644 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 7.22 % Allowed : 19.44 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.11 (0.36), residues: 599 helix: 0.88 (0.55), residues: 107 sheet: -0.03 (0.44), residues: 143 loop : -0.33 (0.36), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 117 HIS 0.004 0.002 HIS A 146 PHE 0.018 0.002 PHE B 144 TYR 0.007 0.001 TYR A 138 ARG 0.002 0.000 ARG C 125 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 33 time to evaluate : 0.459 Fit side-chains REVERT: C 125 ARG cc_start: 0.8265 (ttt90) cc_final: 0.7637 (tmm-80) REVERT: C 137 ARG cc_start: 0.8426 (mtp180) cc_final: 0.7655 (mtp85) REVERT: C 264 PHE cc_start: 0.4708 (m-80) cc_final: 0.4441 (m-80) outliers start: 13 outliers final: 11 residues processed: 42 average time/residue: 0.1324 time to fit residues: 7.4813 Evaluate side-chains 43 residues out of total 489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 32 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 164 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 0.0770 chunk 43 optimal weight: 0.4980 chunk 16 optimal weight: 0.7980 chunk 49 optimal weight: 0.0030 chunk 51 optimal weight: 0.0670 chunk 54 optimal weight: 5.9990 chunk 35 optimal weight: 0.0970 chunk 57 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 0.0770 chunk 60 optimal weight: 9.9990 overall best weight: 0.0642 ------------------------------------------------------------------------------- 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: 0.7569 moved from start: 0.5673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3796 Z= 0.124 Angle : 0.510 11.463 5195 Z= 0.251 Chirality : 0.044 0.131 619 Planarity : 0.003 0.042 718 Dihedral : 3.405 14.143 644 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.44 % Allowed : 21.11 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.29 (0.36), residues: 599 helix: 1.24 (0.55), residues: 108 sheet: 0.24 (0.45), residues: 143 loop : -0.08 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 117 HIS 0.001 0.000 HIS C 282 PHE 0.016 0.001 PHE B 144 TYR 0.011 0.001 TYR B 52 ARG 0.004 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.424 Fit side-chains REVERT: A 196 VAL cc_start: 0.6984 (p) cc_final: 0.6767 (p) REVERT: C 125 ARG cc_start: 0.8080 (ttt90) cc_final: 0.7502 (tmm-80) REVERT: C 137 ARG cc_start: 0.8419 (mtp180) cc_final: 0.7701 (mtp85) REVERT: C 264 PHE cc_start: 0.5152 (m-80) cc_final: 0.4857 (m-80) outliers start: 8 outliers final: 5 residues processed: 42 average time/residue: 0.1271 time to fit residues: 7.2372 Evaluate side-chains 38 residues out of total 489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 33 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 116 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 37 optimal weight: 0.0970 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 0.0030 chunk 51 optimal weight: 10.0000 chunk 14 optimal weight: 0.3980 chunk 44 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 overall best weight: 0.3788 ------------------------------------------------------------------------------- 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: 0.7628 moved from start: 0.5747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3796 Z= 0.167 Angle : 0.524 11.400 5195 Z= 0.259 Chirality : 0.044 0.128 619 Planarity : 0.003 0.041 718 Dihedral : 3.418 14.847 644 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.33 % Allowed : 22.22 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.25 (0.37), residues: 599 helix: 1.06 (0.54), residues: 113 sheet: 0.36 (0.46), residues: 141 loop : -0.16 (0.36), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 117 HIS 0.003 0.001 HIS B 72 PHE 0.017 0.001 PHE B 144 TYR 0.005 0.001 TYR A 138 ARG 0.002 0.000 ARG C 125 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.402 Fit side-chains REVERT: A 196 VAL cc_start: 0.7081 (p) cc_final: 0.6833 (p) REVERT: C 125 ARG cc_start: 0.8198 (ttt90) cc_final: 0.7548 (tmm-80) REVERT: C 137 ARG cc_start: 0.8479 (mtp180) cc_final: 0.7750 (mtp85) REVERT: C 264 PHE cc_start: 0.5137 (m-80) cc_final: 0.4879 (m-80) outliers start: 6 outliers final: 6 residues processed: 39 average time/residue: 0.1270 time to fit residues: 6.7122 Evaluate side-chains 39 residues out of total 489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 137 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 chunk 6 optimal weight: 0.0870 chunk 8 optimal weight: 0.0980 chunk 42 optimal weight: 0.0980 chunk 2 optimal weight: 0.0070 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 overall best weight: 0.2576 ------------------------------------------------------------------------------- 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 = 0.3873 r_free = 0.3873 target = 0.148809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.121330 restraints weight = 7373.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.119634 restraints weight = 7126.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.120600 restraints weight = 5529.272| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.5800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3796 Z= 0.134 Angle : 0.511 12.137 5195 Z= 0.248 Chirality : 0.043 0.129 619 Planarity : 0.003 0.042 718 Dihedral : 3.186 13.725 644 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.78 % Allowed : 22.78 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.39 (0.37), residues: 599 helix: 1.12 (0.54), residues: 114 sheet: 0.47 (0.45), residues: 143 loop : -0.05 (0.36), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 117 HIS 0.002 0.001 HIS A 146 PHE 0.016 0.001 PHE B 144 TYR 0.006 0.001 TYR A 138 ARG 0.003 0.000 ARG C 125 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1167.82 seconds wall clock time: 21 minutes 34.41 seconds (1294.41 seconds total)