Starting phenix.real_space_refine on Fri Aug 2 17:00:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w22_43737/08_2024/8w22_43737.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w22_43737/08_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_43737/08_2024/8w22_43737.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w22_43737/08_2024/8w22_43737.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w22_43737/08_2024/8w22_43737.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w22_43737/08_2024/8w22_43737.cif" } 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-5409/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: 3.02, per 1000 atoms: 0.81 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: 1.25 Conformation dependent library (CDL) restraints added in 772.6 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: 0.52 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: 1.26 Time building geometry restraints manager: 1.40 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 3.120 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 Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.170 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.980 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.260 ------------------------------------------------------------------------------- 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 : 0.437 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: 0.2041 time to fit residues: 17.4944 Evaluate side-chains 41 residues out of total 489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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: 10.0000 chunk 46 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 0.3980 chunk 47 optimal weight: 0.3980 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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: 0.7566 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3796 Z= 0.292 Angle : 0.619 5.445 5195 Z= 0.339 Chirality : 0.047 0.163 619 Planarity : 0.005 0.028 718 Dihedral : 4.303 18.740 644 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.33 % Allowed : 14.44 % 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: 0.83 (0.36), residues: 599 helix: 0.85 (0.49), residues: 115 sheet: 0.98 (0.42), residues: 169 loop : 0.31 (0.38), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 117 HIS 0.002 0.001 HIS C 116 PHE 0.016 0.002 PHE C 171 TYR 0.017 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 50 residues out of total 489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.422 Fit side-chains REVERT: A 106 ARG cc_start: 0.5686 (ttm110) cc_final: 0.4961 (tpp-160) REVERT: A 156 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8513 (tt) REVERT: B 100 MET cc_start: 0.9075 (mmm) cc_final: 0.8731 (mmt) REVERT: C 125 ARG cc_start: 0.7899 (ttt180) cc_final: 0.7656 (tmt-80) REVERT: C 137 ARG cc_start: 0.7837 (mtp180) cc_final: 0.7413 (mtp85) outliers start: 6 outliers final: 4 residues processed: 48 average time/residue: 0.1370 time to fit residues: 8.6851 Evaluate side-chains 44 residues out of total 489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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: 0.6980 chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 0.0030 chunk 37 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 55 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 18 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN B 92 GLN C 167 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3796 Z= 0.205 Angle : 0.517 5.284 5195 Z= 0.276 Chirality : 0.045 0.131 619 Planarity : 0.004 0.033 718 Dihedral : 3.799 15.431 644 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.44 % Allowed : 17.22 % Favored : 78.33 % 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: 0.84 (0.36), residues: 599 helix: 1.37 (0.53), residues: 110 sheet: 0.82 (0.42), residues: 168 loop : 0.23 (0.38), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 117 HIS 0.003 0.001 HIS B 72 PHE 0.019 0.002 PHE C 171 TYR 0.008 0.001 TYR A 185 ARG 0.003 0.000 ARG A 193 *********************** 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 53 residues out of total 489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.438 Fit side-chains REVERT: B 100 MET cc_start: 0.9109 (mmm) cc_final: 0.8863 (mmm) REVERT: C 121 MET cc_start: 0.7071 (mmm) cc_final: 0.6798 (tpp) REVERT: C 137 ARG cc_start: 0.8034 (mtp180) cc_final: 0.7537 (mtp85) outliers start: 8 outliers final: 5 residues processed: 49 average time/residue: 0.1260 time to fit residues: 8.5560 Evaluate side-chains 44 residues out of total 489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 137 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 0.0170 chunk 37 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 52 optimal weight: 20.0000 chunk 15 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 overall best weight: 1.1622 ------------------------------------------------------------------------------- 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: 0.7731 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 3796 Z= 0.412 Angle : 0.659 6.095 5195 Z= 0.360 Chirality : 0.049 0.167 619 Planarity : 0.005 0.034 718 Dihedral : 4.810 19.218 644 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 6.11 % Allowed : 14.44 % Favored : 79.44 % 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: 0.12 (0.36), residues: 599 helix: 0.60 (0.52), residues: 108 sheet: 0.54 (0.44), residues: 154 loop : -0.25 (0.36), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 117 HIS 0.007 0.002 HIS B 72 PHE 0.017 0.003 PHE B 97 TYR 0.018 0.002 TYR A 185 ARG 0.003 0.001 ARG A 152 *********************** 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 50 residues out of total 489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 39 time to evaluate : 0.443 Fit side-chains REVERT: B 100 MET cc_start: 0.8868 (mmm) cc_final: 0.8610 (mmm) REVERT: C 121 MET cc_start: 0.6985 (mmm) cc_final: 0.6630 (tpp) REVERT: C 137 ARG cc_start: 0.8339 (mtp180) cc_final: 0.7659 (mtp85) REVERT: C 264 PHE cc_start: 0.5953 (m-80) cc_final: 0.5690 (m-80) outliers start: 11 outliers final: 6 residues processed: 46 average time/residue: 0.1224 time to fit residues: 7.6582 Evaluate side-chains 44 residues out of total 489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 66 LEU 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: 10.0000 chunk 24 optimal weight: 0.2980 chunk 50 optimal weight: 0.0170 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 52 optimal weight: 20.0000 chunk 14 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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: 0.7650 moved from start: 0.4836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3796 Z= 0.196 Angle : 0.515 6.598 5195 Z= 0.271 Chirality : 0.045 0.135 619 Planarity : 0.004 0.039 718 Dihedral : 3.881 15.547 644 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.44 % Allowed : 17.78 % Favored : 77.78 % 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: 0.37 (0.37), residues: 599 helix: 1.11 (0.55), residues: 109 sheet: 0.45 (0.43), residues: 154 loop : -0.07 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 117 HIS 0.004 0.001 HIS B 72 PHE 0.016 0.002 PHE C 171 TYR 0.006 0.001 TYR A 138 ARG 0.003 0.000 ARG A 193 *********************** 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 46 residues out of total 489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 0.444 Fit side-chains REVERT: C 121 MET cc_start: 0.7141 (mmm) cc_final: 0.6823 (tpp) REVERT: C 125 ARG cc_start: 0.8022 (ttt90) cc_final: 0.7448 (tmm-80) REVERT: C 137 ARG cc_start: 0.8267 (mtp180) cc_final: 0.7568 (mtp85) outliers start: 8 outliers final: 5 residues processed: 45 average time/residue: 0.1268 time to fit residues: 7.7900 Evaluate side-chains 42 residues out of total 489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 37 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 14 optimal weight: 0.2980 chunk 59 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 27 optimal weight: 0.8980 chunk 4 optimal weight: 0.4980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 6 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.7673 moved from start: 0.5143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3796 Z= 0.226 Angle : 0.526 6.932 5195 Z= 0.277 Chirality : 0.045 0.143 619 Planarity : 0.004 0.039 718 Dihedral : 3.835 16.005 644 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 5.56 % Allowed : 16.67 % Favored : 77.78 % 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: 0.40 (0.37), residues: 599 helix: 1.08 (0.55), residues: 109 sheet: 0.40 (0.43), residues: 154 loop : 0.01 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 117 HIS 0.004 0.001 HIS B 72 PHE 0.014 0.002 PHE C 171 TYR 0.008 0.001 TYR A 185 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: 10 poor density : 39 time to evaluate : 0.431 Fit side-chains REVERT: C 121 MET cc_start: 0.7136 (mmm) cc_final: 0.6853 (tpp) REVERT: C 125 ARG cc_start: 0.8078 (ttt90) cc_final: 0.7432 (tmm-80) REVERT: C 137 ARG cc_start: 0.8352 (mtp180) cc_final: 0.7621 (mtp85) outliers start: 10 outliers final: 8 residues processed: 47 average time/residue: 0.1223 time to fit residues: 7.8055 Evaluate side-chains 42 residues out of total 489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 34 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 43 optimal weight: 0.0040 chunk 49 optimal weight: 9.9990 chunk 32 optimal weight: 0.0470 chunk 58 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 27 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.3890 ------------------------------------------------------------------------------- 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: 0.7630 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3796 Z= 0.170 Angle : 0.493 7.163 5195 Z= 0.254 Chirality : 0.044 0.129 619 Planarity : 0.003 0.042 718 Dihedral : 3.552 14.291 644 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.33 % Allowed : 21.67 % Favored : 75.00 % 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: 0.43 (0.37), residues: 599 helix: 1.21 (0.55), residues: 109 sheet: 0.42 (0.45), residues: 143 loop : 0.02 (0.37), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 117 HIS 0.003 0.001 HIS B 72 PHE 0.016 0.002 PHE C 171 TYR 0.006 0.001 TYR A 138 ARG 0.003 0.000 ARG C 125 *********************** 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 42 residues out of total 489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 36 time to evaluate : 0.427 Fit side-chains REVERT: C 121 MET cc_start: 0.7112 (mmm) cc_final: 0.6863 (tpp) REVERT: C 125 ARG cc_start: 0.8171 (ttt90) cc_final: 0.7567 (tmm-80) REVERT: C 137 ARG cc_start: 0.8331 (mtp180) cc_final: 0.7599 (mtp85) outliers start: 6 outliers final: 5 residues processed: 42 average time/residue: 0.1221 time to fit residues: 6.9909 Evaluate side-chains 39 residues out of total 489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 29 optimal weight: 0.0980 chunk 5 optimal weight: 0.0980 chunk 46 optimal weight: 0.2980 chunk 53 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 54 optimal weight: 0.1980 chunk 32 optimal weight: 0.9990 overall best weight: 0.2580 ------------------------------------------------------------------------------- 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: 0.7597 moved from start: 0.5320 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= 0.136 Angle : 0.475 8.309 5195 Z= 0.239 Chirality : 0.043 0.127 619 Planarity : 0.003 0.045 718 Dihedral : 3.221 12.802 644 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.33 % Allowed : 20.56 % Favored : 76.11 % 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: 0.64 (0.37), residues: 599 helix: 1.06 (0.54), residues: 116 sheet: 0.30 (0.43), residues: 151 loop : 0.39 (0.38), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 117 HIS 0.002 0.001 HIS A 146 PHE 0.013 0.001 PHE C 171 TYR 0.005 0.001 TYR A 138 ARG 0.003 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 42 residues out of total 489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 36 time to evaluate : 0.426 Fit side-chains REVERT: B 112 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8475 (mp10) REVERT: C 121 MET cc_start: 0.7094 (mmm) cc_final: 0.6873 (tpp) REVERT: C 125 ARG cc_start: 0.8131 (ttt90) cc_final: 0.7523 (tmm-80) REVERT: C 137 ARG cc_start: 0.8331 (mtp180) cc_final: 0.7604 (mtp85) outliers start: 6 outliers final: 4 residues processed: 42 average time/residue: 0.1243 time to fit residues: 7.1101 Evaluate side-chains 40 residues out of total 489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 35 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 PHE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 3.9990 chunk 43 optimal weight: 0.0010 chunk 16 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 57 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 overall best weight: 1.5592 ------------------------------------------------------------------------------- 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: 0.7788 moved from start: 0.5813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 3796 Z= 0.530 Angle : 0.729 7.275 5195 Z= 0.395 Chirality : 0.051 0.186 619 Planarity : 0.005 0.035 718 Dihedral : 4.908 19.394 644 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 4.44 % Allowed : 20.56 % Favored : 75.00 % 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: -0.02 (0.51), residues: 120 sheet: 0.01 (0.43), residues: 144 loop : -0.24 (0.37), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 117 HIS 0.008 0.003 HIS B 72 PHE 0.022 0.003 PHE B 97 TYR 0.012 0.002 TYR A 185 ARG 0.004 0.001 ARG A 162 *********************** 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 40 residues out of total 489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 32 time to evaluate : 0.425 Fit side-chains REVERT: A 196 VAL cc_start: 0.7209 (p) cc_final: 0.6864 (p) REVERT: C 121 MET cc_start: 0.7055 (mmm) cc_final: 0.6748 (tpp) REVERT: C 125 ARG cc_start: 0.8332 (ttt90) cc_final: 0.7714 (tmm-80) REVERT: C 137 ARG cc_start: 0.8494 (mtp180) cc_final: 0.7728 (mtp85) outliers start: 8 outliers final: 8 residues processed: 40 average time/residue: 0.1272 time to fit residues: 6.9441 Evaluate side-chains 39 residues out of total 489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 31 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 186 THR Chi-restraints excluded: chain B residue 95 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 37 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 0.0570 chunk 51 optimal weight: 8.9990 chunk 14 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 13 optimal weight: 0.3980 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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: 0.7682 moved from start: 0.5771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3796 Z= 0.210 Angle : 0.531 7.766 5195 Z= 0.277 Chirality : 0.045 0.130 619 Planarity : 0.004 0.044 718 Dihedral : 3.949 16.473 644 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.44 % Allowed : 20.56 % Favored : 75.00 % 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: -0.04 (0.36), residues: 599 helix: 0.85 (0.55), residues: 109 sheet: 0.01 (0.43), residues: 142 loop : -0.25 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 117 HIS 0.004 0.001 HIS B 72 PHE 0.019 0.002 PHE C 171 TYR 0.009 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 40 residues out of total 489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 32 time to evaluate : 0.434 Fit side-chains REVERT: A 196 VAL cc_start: 0.6839 (p) cc_final: 0.6518 (p) REVERT: C 121 MET cc_start: 0.6982 (mmm) cc_final: 0.6709 (tpp) REVERT: C 125 ARG cc_start: 0.8178 (ttt90) cc_final: 0.7505 (tmm-80) REVERT: C 137 ARG cc_start: 0.8433 (mtp180) cc_final: 0.7699 (mtp85) outliers start: 8 outliers final: 7 residues processed: 40 average time/residue: 0.1315 time to fit residues: 7.2452 Evaluate side-chains 39 residues out of total 489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 32 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain B residue 95 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 10.0000 chunk 20 optimal weight: 0.3980 chunk 49 optimal weight: 5.9990 chunk 6 optimal weight: 0.2980 chunk 8 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3821 r_free = 0.3821 target = 0.144657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.117149 restraints weight = 7396.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.117210 restraints weight = 6695.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.117729 restraints weight = 6233.000| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.5876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3796 Z= 0.232 Angle : 0.536 7.656 5195 Z= 0.280 Chirality : 0.045 0.147 619 Planarity : 0.004 0.043 718 Dihedral : 3.851 15.769 644 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.89 % Allowed : 20.56 % 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: -0.01 (0.36), residues: 599 helix: 0.82 (0.54), residues: 113 sheet: -0.00 (0.44), residues: 142 loop : -0.21 (0.37), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 117 HIS 0.005 0.001 HIS B 72 PHE 0.016 0.002 PHE C 171 TYR 0.005 0.001 TYR A 185 ARG 0.002 0.000 ARG C 125 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1148.88 seconds wall clock time: 20 minutes 44.79 seconds (1244.79 seconds total)