Starting phenix.real_space_refine on Fri Aug 2 17:52:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v3q_42950/08_2024/8v3q_42950.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v3q_42950/08_2024/8v3q_42950.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v3q_42950/08_2024/8v3q_42950.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v3q_42950/08_2024/8v3q_42950.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v3q_42950/08_2024/8v3q_42950.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v3q_42950/08_2024/8v3q_42950.cif" } resolution = 3.1 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= 0.001 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 22 5.16 5 C 2556 2.51 5 N 722 2.21 5 O 729 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 5": not complete - not flipped Residue "M GLU 1001": "OE1" <-> "OE2" 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: 4030 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3971 Classifications: {'peptide': 501} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 35, 'TRANS': 465} Chain breaks: 3 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 57 Chain: "M" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 48 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 3.74, per 1000 atoms: 0.93 Number of scatterers: 4030 At special positions: 0 Unit cell: (77.19, 73.455, 69.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 22 16.00 O 729 8.00 N 722 7.00 C 2556 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 610.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" ND1 HIS A 252 " pdb="ZN ZN A 701 " - pdb=" ND1 HIS A 434 " 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 960 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 4 sheets defined 30.6% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 98 through 104 Processing helix chain 'A' and resid 160 through 175 Processing helix chain 'A' and resid 256 through 270 removed outlier: 3.766A pdb=" N PHE A 260 " --> pdb=" O THR A 256 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 310 through 315 removed outlier: 3.892A pdb=" N TYR A 315 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 340 Processing helix chain 'A' and resid 451 through 467 removed outlier: 4.338A pdb=" N TYR A 461 " --> pdb=" O GLU A 457 " (cutoff:3.500A) Proline residue: A 462 - end of helix Processing helix chain 'A' and resid 481 through 485 Processing helix chain 'A' and resid 494 through 497 removed outlier: 3.559A pdb=" N GLY A 497 " --> pdb=" O SER A 494 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 494 through 497' Processing helix chain 'A' and resid 498 through 508 removed outlier: 3.573A pdb=" N TYR A 504 " --> pdb=" O ARG A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 570 removed outlier: 3.685A pdb=" N ALA A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 601 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5 removed outlier: 3.635A pdb=" N ARG A 111 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N THR A 112 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ARG A 118 " --> pdb=" O THR A 112 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 24 removed outlier: 3.501A pdb=" N HIS A 21 " --> pdb=" O TRP A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 189 through 198 removed outlier: 7.283A pdb=" N VAL A 205 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N SER A 212 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N PHE A 284 " --> pdb=" O SER A 212 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ARG A 243 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LYS A 287 " --> pdb=" O ARG A 243 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N PHE A 245 " --> pdb=" O LYS A 287 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE A 289 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU A 247 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE A 244 " --> pdb=" O TYR A 429 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N VAL A 431 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE A 246 " --> pdb=" O VAL A 431 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LEU A 433 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N SER A 248 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N GLY A 435 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 216 through 220 removed outlier: 3.714A pdb=" N ARG A 238 " --> pdb=" O ARG A 217 " (cutoff:3.500A) 151 hydrogen bonds defined for protein. 426 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: 1.10 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 642 1.31 - 1.43: 1209 1.43 - 1.56: 2249 1.56 - 1.68: 7 1.68 - 1.81: 33 Bond restraints: 4140 Sorted by residual: bond pdb=" C GLU M 5 " pdb=" O GLU M 5 " ideal model delta sigma weight residual 1.231 1.181 0.050 2.00e-02 2.50e+03 6.26e+00 bond pdb=" CB VAL A 261 " pdb=" CG2 VAL A 261 " ideal model delta sigma weight residual 1.521 1.441 0.080 3.30e-02 9.18e+02 5.89e+00 bond pdb=" C SER A 184 " pdb=" N PRO A 185 " ideal model delta sigma weight residual 1.334 1.385 -0.051 2.34e-02 1.83e+03 4.71e+00 bond pdb=" C THR A 256 " pdb=" N PRO A 257 " ideal model delta sigma weight residual 1.335 1.362 -0.027 1.28e-02 6.10e+03 4.60e+00 bond pdb=" C PHE A 546 " pdb=" N PRO A 547 " ideal model delta sigma weight residual 1.336 1.362 -0.026 1.23e-02 6.61e+03 4.60e+00 ... (remaining 4135 not shown) Histogram of bond angle deviations from ideal: 96.68 - 104.24: 92 104.24 - 111.80: 1726 111.80 - 119.36: 1647 119.36 - 126.92: 2081 126.92 - 134.48: 70 Bond angle restraints: 5616 Sorted by residual: angle pdb=" C SER A 183 " pdb=" N SER A 184 " pdb=" CA SER A 184 " ideal model delta sigma weight residual 120.51 129.21 -8.70 1.45e+00 4.76e-01 3.60e+01 angle pdb=" C LYS A 495 " pdb=" N GLU A 496 " pdb=" CA GLU A 496 " ideal model delta sigma weight residual 120.82 128.43 -7.61 1.50e+00 4.44e-01 2.58e+01 angle pdb=" CG ARG A 549 " pdb=" CD ARG A 549 " pdb=" NE ARG A 549 " ideal model delta sigma weight residual 112.00 120.77 -8.77 2.20e+00 2.07e-01 1.59e+01 angle pdb=" N THR A 256 " pdb=" CA THR A 256 " pdb=" C THR A 256 " ideal model delta sigma weight residual 109.81 118.50 -8.69 2.21e+00 2.05e-01 1.55e+01 angle pdb=" C MET A 130 " pdb=" N THR A 131 " pdb=" CA THR A 131 " ideal model delta sigma weight residual 120.82 126.56 -5.74 1.47e+00 4.63e-01 1.53e+01 ... (remaining 5611 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.43: 2315 22.43 - 44.86: 127 44.86 - 67.29: 18 67.29 - 89.72: 3 89.72 - 112.15: 1 Dihedral angle restraints: 2464 sinusoidal: 978 harmonic: 1486 Sorted by residual: dihedral pdb=" CB GLU M 5 " pdb=" CG GLU M 5 " pdb=" CD GLU M 5 " pdb=" OE1 GLU M 5 " ideal model delta sinusoidal sigma weight residual 0.00 112.15 -112.15 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" CA MET A 444 " pdb=" C MET A 444 " pdb=" N TYR A 445 " pdb=" CA TYR A 445 " ideal model delta harmonic sigma weight residual 180.00 162.05 17.95 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA TYR A 429 " pdb=" C TYR A 429 " pdb=" N TYR A 430 " pdb=" CA TYR A 430 " ideal model delta harmonic sigma weight residual 180.00 162.43 17.57 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 2461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 483 0.089 - 0.178: 93 0.178 - 0.267: 14 0.267 - 0.356: 1 0.356 - 0.444: 2 Chirality restraints: 593 Sorted by residual: chirality pdb=" CB VAL A 25 " pdb=" CA VAL A 25 " pdb=" CG1 VAL A 25 " pdb=" CG2 VAL A 25 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.44 2.00e-01 2.50e+01 4.94e+00 chirality pdb=" CA GLU M1001 " pdb=" N GLU M1001 " pdb=" C GLU M1001 " pdb=" CB GLU M1001 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" CB VAL A 261 " pdb=" CA VAL A 261 " pdb=" CG1 VAL A 261 " pdb=" CG2 VAL A 261 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.72e+00 ... (remaining 590 not shown) Planarity restraints: 741 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 317 " -0.018 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C LYS A 317 " 0.060 2.00e-02 2.50e+03 pdb=" O LYS A 317 " -0.023 2.00e-02 2.50e+03 pdb=" N PRO A 318 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 258 " -0.017 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C SER A 258 " 0.057 2.00e-02 2.50e+03 pdb=" O SER A 258 " -0.021 2.00e-02 2.50e+03 pdb=" N SER A 259 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 311 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.10e+00 pdb=" C LEU A 311 " 0.052 2.00e-02 2.50e+03 pdb=" O LEU A 311 " -0.019 2.00e-02 2.50e+03 pdb=" N ASN A 312 " -0.018 2.00e-02 2.50e+03 ... (remaining 738 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.08: 1 2.08 - 2.78: 843 2.78 - 3.49: 5289 3.49 - 4.19: 9837 4.19 - 4.90: 17444 Nonbonded interactions: 33414 Sorted by model distance: nonbonded pdb=" CD GLU M 5 " pdb=" N GLU M1001 " model vdw 1.370 3.350 nonbonded pdb=" OE1 GLU A 255 " pdb="ZN ZN A 701 " model vdw 2.109 2.230 nonbonded pdb=" OE1 GLU M 5 " pdb="ZN ZN A 701 " model vdw 2.111 2.230 nonbonded pdb=" OE2 GLU A 255 " pdb="ZN ZN A 701 " model vdw 2.145 2.230 nonbonded pdb=" OE1 GLU M 5 " pdb=" N GLU M1001 " model vdw 2.275 3.120 ... (remaining 33409 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.090 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.680 Find NCS groups from input model: 0.030 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 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 : 0.009 0.092 4140 Z= 0.600 Angle : 1.223 9.703 5616 Z= 0.680 Chirality : 0.074 0.444 593 Planarity : 0.010 0.059 741 Dihedral : 14.292 112.148 1504 Min Nonbonded Distance : 1.370 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.34), residues: 493 helix: -1.49 (0.34), residues: 140 sheet: 0.93 (0.58), residues: 80 loop : -1.04 (0.34), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 592 HIS 0.026 0.003 HIS A 533 PHE 0.023 0.004 PHE A 262 TYR 0.030 0.004 TYR A 430 ARG 0.017 0.002 ARG A 549 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.391 Fit side-chains REVERT: A 3 LEU cc_start: 0.7710 (mt) cc_final: 0.7418 (mp) REVERT: A 13 ARG cc_start: 0.8054 (ttp-170) cc_final: 0.7749 (ttm170) REVERT: A 69 ASN cc_start: 0.8022 (m-40) cc_final: 0.7817 (m110) REVERT: A 118 ARG cc_start: 0.7980 (ttt-90) cc_final: 0.7685 (ttt90) REVERT: A 120 GLU cc_start: 0.8158 (pt0) cc_final: 0.7580 (pt0) REVERT: A 166 GLU cc_start: 0.7140 (tp30) cc_final: 0.6499 (tt0) REVERT: A 169 ASN cc_start: 0.7551 (m-40) cc_final: 0.6882 (m-40) REVERT: A 170 GLN cc_start: 0.7255 (mm-40) cc_final: 0.6816 (mt0) REVERT: A 172 ASP cc_start: 0.7329 (t0) cc_final: 0.7083 (t0) REVERT: A 226 GLN cc_start: 0.8105 (tt0) cc_final: 0.7481 (tp-100) REVERT: A 475 GLN cc_start: 0.8457 (mp10) cc_final: 0.8081 (mp10) REVERT: A 481 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7552 (mm-30) REVERT: A 595 LYS cc_start: 0.6603 (ttpt) cc_final: 0.5689 (mttt) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.2387 time to fit residues: 18.7182 Evaluate side-chains 47 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 0.0980 chunk 12 optimal weight: 0.3980 chunk 25 optimal weight: 0.0770 chunk 20 optimal weight: 0.0070 chunk 39 optimal weight: 0.9980 chunk 15 optimal weight: 0.3980 chunk 23 optimal weight: 0.0870 chunk 29 optimal weight: 0.0770 chunk 45 optimal weight: 0.4980 overall best weight: 0.0692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 HIS A 533 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4140 Z= 0.157 Angle : 0.548 5.251 5616 Z= 0.287 Chirality : 0.041 0.146 593 Planarity : 0.005 0.041 741 Dihedral : 5.451 66.558 567 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.41 % Allowed : 9.62 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.37), residues: 493 helix: 0.38 (0.42), residues: 140 sheet: 0.67 (0.56), residues: 90 loop : -0.50 (0.38), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 592 HIS 0.008 0.001 HIS A 533 PHE 0.011 0.001 PHE A 152 TYR 0.008 0.001 TYR A 102 ARG 0.005 0.000 ARG A 549 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 0.452 Fit side-chains REVERT: A 13 ARG cc_start: 0.8199 (ttp-170) cc_final: 0.7912 (ttm170) REVERT: A 69 ASN cc_start: 0.7892 (m-40) cc_final: 0.7653 (m-40) REVERT: A 130 MET cc_start: 0.8251 (tpt) cc_final: 0.8026 (tpp) REVERT: A 133 THR cc_start: 0.7792 (p) cc_final: 0.7538 (t) REVERT: A 166 GLU cc_start: 0.7166 (tp30) cc_final: 0.6578 (tt0) REVERT: A 169 ASN cc_start: 0.7225 (m-40) cc_final: 0.6634 (m-40) REVERT: A 170 GLN cc_start: 0.7248 (mm-40) cc_final: 0.6922 (mt0) REVERT: A 190 TYR cc_start: 0.8550 (t80) cc_final: 0.8003 (t80) REVERT: A 424 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7152 (tt0) REVERT: A 595 LYS cc_start: 0.6647 (ttpt) cc_final: 0.5643 (mttt) outliers start: 6 outliers final: 3 residues processed: 58 average time/residue: 0.2209 time to fit residues: 16.1456 Evaluate side-chains 47 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 532 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 30 optimal weight: 0.0870 chunk 12 optimal weight: 0.6980 chunk 45 optimal weight: 0.2980 chunk 49 optimal weight: 0.2980 chunk 40 optimal weight: 0.0970 chunk 15 optimal weight: 0.6980 chunk 36 optimal weight: 0.0980 chunk 44 optimal weight: 0.0010 overall best weight: 0.1162 ------------------------------------------------------------------------------- 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: 0.7375 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4140 Z= 0.175 Angle : 0.520 5.174 5616 Z= 0.268 Chirality : 0.040 0.152 593 Planarity : 0.004 0.037 741 Dihedral : 5.045 60.956 567 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.41 % Allowed : 11.27 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.38), residues: 493 helix: 1.07 (0.44), residues: 140 sheet: 0.73 (0.56), residues: 92 loop : -0.27 (0.40), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 592 HIS 0.003 0.001 HIS A 533 PHE 0.009 0.001 PHE A 284 TYR 0.010 0.001 TYR A 102 ARG 0.004 0.000 ARG A 549 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.408 Fit side-chains REVERT: A 13 ARG cc_start: 0.8220 (ttp-170) cc_final: 0.7908 (ttm170) REVERT: A 69 ASN cc_start: 0.7992 (m-40) cc_final: 0.7708 (m-40) REVERT: A 130 MET cc_start: 0.8238 (tpt) cc_final: 0.8035 (tpp) REVERT: A 166 GLU cc_start: 0.7216 (tp30) cc_final: 0.6591 (tt0) REVERT: A 169 ASN cc_start: 0.7177 (m-40) cc_final: 0.6800 (m-40) REVERT: A 170 GLN cc_start: 0.7269 (mm-40) cc_final: 0.6913 (mt0) REVERT: A 424 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7157 (tt0) REVERT: A 459 MET cc_start: 0.8523 (mtm) cc_final: 0.8241 (mtm) REVERT: A 595 LYS cc_start: 0.6612 (ttpt) cc_final: 0.5667 (mttt) outliers start: 6 outliers final: 3 residues processed: 52 average time/residue: 0.1909 time to fit residues: 12.1891 Evaluate side-chains 45 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 431 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 0.5980 chunk 23 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 0.2980 chunk 30 optimal weight: 0.9980 chunk 45 optimal weight: 0.1980 chunk 48 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 13 optimal weight: 0.0770 chunk 40 optimal weight: 0.0870 chunk 27 optimal weight: 0.0970 overall best weight: 0.1514 ------------------------------------------------------------------------------- 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: 0.7395 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4140 Z= 0.194 Angle : 0.514 5.196 5616 Z= 0.263 Chirality : 0.041 0.157 593 Planarity : 0.004 0.035 741 Dihedral : 5.005 63.794 567 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.11 % Allowed : 10.33 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.39), residues: 493 helix: 1.60 (0.45), residues: 140 sheet: 0.72 (0.57), residues: 92 loop : -0.20 (0.40), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 592 HIS 0.003 0.001 HIS A 336 PHE 0.009 0.001 PHE A 265 TYR 0.012 0.001 TYR A 102 ARG 0.005 0.000 ARG A 549 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.456 Fit side-chains REVERT: A 13 ARG cc_start: 0.8180 (ttp-170) cc_final: 0.7904 (ttm170) REVERT: A 166 GLU cc_start: 0.7245 (tp30) cc_final: 0.6706 (tt0) REVERT: A 169 ASN cc_start: 0.7140 (m-40) cc_final: 0.6823 (m-40) REVERT: A 170 GLN cc_start: 0.7256 (mm-40) cc_final: 0.6909 (mt0) REVERT: A 424 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7211 (tt0) REVERT: A 459 MET cc_start: 0.8599 (mtm) cc_final: 0.8353 (mtm) REVERT: A 496 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7698 (tm-30) REVERT: A 523 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8630 (mtm-85) REVERT: A 569 MET cc_start: 0.7138 (OUTLIER) cc_final: 0.6913 (mtp) REVERT: A 595 LYS cc_start: 0.6606 (ttpt) cc_final: 0.5669 (mttt) outliers start: 9 outliers final: 3 residues processed: 50 average time/residue: 0.2317 time to fit residues: 13.9791 Evaluate side-chains 47 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 523 ARG Chi-restraints excluded: chain A residue 532 CYS Chi-restraints excluded: chain A residue 569 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 19 optimal weight: 0.0870 chunk 41 optimal weight: 0.2980 chunk 33 optimal weight: 0.0980 chunk 24 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 16 optimal weight: 0.2980 chunk 9 optimal weight: 0.2980 chunk 28 optimal weight: 0.7980 overall best weight: 0.2158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 533 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4140 Z= 0.247 Angle : 0.538 5.403 5616 Z= 0.276 Chirality : 0.042 0.164 593 Planarity : 0.004 0.032 741 Dihedral : 5.270 71.532 567 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.82 % Allowed : 9.62 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.39), residues: 493 helix: 1.70 (0.46), residues: 140 sheet: 1.02 (0.58), residues: 88 loop : -0.15 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 592 HIS 0.004 0.001 HIS A 336 PHE 0.010 0.002 PHE A 128 TYR 0.015 0.002 TYR A 102 ARG 0.004 0.000 ARG A 549 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 40 time to evaluate : 0.458 Fit side-chains REVERT: A 13 ARG cc_start: 0.8205 (ttp-170) cc_final: 0.7955 (ttm170) REVERT: A 116 ARG cc_start: 0.7264 (ttp-110) cc_final: 0.6839 (mtm180) REVERT: A 166 GLU cc_start: 0.7398 (tp30) cc_final: 0.6880 (tt0) REVERT: A 169 ASN cc_start: 0.7159 (m-40) cc_final: 0.6808 (m-40) REVERT: A 170 GLN cc_start: 0.7145 (mm-40) cc_final: 0.6792 (mt0) REVERT: A 424 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7151 (tt0) REVERT: A 459 MET cc_start: 0.8618 (mtm) cc_final: 0.8380 (mtm) REVERT: A 496 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7974 (tm-30) REVERT: A 523 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8621 (mtm-85) REVERT: A 549 ARG cc_start: 0.8152 (mtm-85) cc_final: 0.7679 (mtt-85) REVERT: A 595 LYS cc_start: 0.6712 (ttpt) cc_final: 0.6295 (tppt) outliers start: 12 outliers final: 6 residues processed: 50 average time/residue: 0.2227 time to fit residues: 13.4771 Evaluate side-chains 46 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 37 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 523 ARG Chi-restraints excluded: chain A residue 569 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 0.5980 chunk 48 optimal weight: 0.2980 chunk 40 optimal weight: 0.0980 chunk 22 optimal weight: 0.8980 chunk 4 optimal weight: 0.0970 chunk 16 optimal weight: 0.4980 chunk 25 optimal weight: 0.0050 chunk 46 optimal weight: 0.0980 chunk 5 optimal weight: 0.5980 chunk 27 optimal weight: 0.0770 chunk 35 optimal weight: 0.6980 overall best weight: 0.0750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4140 Z= 0.141 Angle : 0.489 5.242 5616 Z= 0.248 Chirality : 0.039 0.146 593 Planarity : 0.003 0.032 741 Dihedral : 5.112 74.984 567 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.88 % Allowed : 11.50 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.40), residues: 493 helix: 1.91 (0.46), residues: 140 sheet: 0.88 (0.57), residues: 88 loop : -0.18 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 592 HIS 0.004 0.001 HIS A 533 PHE 0.012 0.001 PHE A 128 TYR 0.009 0.001 TYR A 157 ARG 0.002 0.000 ARG A 549 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.475 Fit side-chains REVERT: A 13 ARG cc_start: 0.8178 (ttp-170) cc_final: 0.7844 (ttm170) REVERT: A 116 ARG cc_start: 0.7239 (ttp-110) cc_final: 0.6840 (mtm180) REVERT: A 166 GLU cc_start: 0.7347 (tp30) cc_final: 0.6884 (tt0) REVERT: A 169 ASN cc_start: 0.7157 (m-40) cc_final: 0.6805 (m-40) REVERT: A 170 GLN cc_start: 0.7181 (mm-40) cc_final: 0.6862 (mt0) REVERT: A 190 TYR cc_start: 0.8781 (t80) cc_final: 0.8216 (t80) REVERT: A 424 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7155 (tt0) REVERT: A 459 MET cc_start: 0.8525 (mtm) cc_final: 0.8261 (mtm) REVERT: A 496 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7982 (tm-30) REVERT: A 523 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8622 (mtm-85) REVERT: A 549 ARG cc_start: 0.8101 (mtm-85) cc_final: 0.7658 (mtt-85) REVERT: A 595 LYS cc_start: 0.6632 (ttpt) cc_final: 0.6273 (tppt) outliers start: 8 outliers final: 2 residues processed: 46 average time/residue: 0.2338 time to fit residues: 12.9831 Evaluate side-chains 43 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 38 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 523 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.0970 chunk 40 optimal weight: 0.3980 chunk 48 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 29 optimal weight: 0.0980 chunk 22 optimal weight: 0.6980 chunk 19 optimal weight: 0.2980 chunk 28 optimal weight: 0.6980 chunk 14 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.2778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 1 ASN A 336 HIS A 533 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 4140 Z= 0.303 Angle : 0.559 5.553 5616 Z= 0.284 Chirality : 0.043 0.171 593 Planarity : 0.004 0.032 741 Dihedral : 5.357 76.696 567 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.58 % Allowed : 10.80 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.39), residues: 493 helix: 1.80 (0.46), residues: 141 sheet: 1.04 (0.57), residues: 86 loop : -0.22 (0.40), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 592 HIS 0.004 0.001 HIS A 336 PHE 0.013 0.002 PHE A 128 TYR 0.016 0.002 TYR A 102 ARG 0.003 0.000 ARG A 549 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 35 time to evaluate : 0.483 Fit side-chains REVERT: A 116 ARG cc_start: 0.7191 (ttp-110) cc_final: 0.6750 (mtm180) REVERT: A 166 GLU cc_start: 0.7348 (tp30) cc_final: 0.6896 (tt0) REVERT: A 169 ASN cc_start: 0.7118 (m-40) cc_final: 0.6785 (m-40) REVERT: A 170 GLN cc_start: 0.7095 (mm-40) cc_final: 0.6815 (mt0) REVERT: A 424 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7126 (tt0) REVERT: A 459 MET cc_start: 0.8567 (mtm) cc_final: 0.8321 (mtm) REVERT: A 496 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8030 (tm-30) REVERT: A 523 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8580 (mtm-85) REVERT: A 549 ARG cc_start: 0.8189 (mtm-85) cc_final: 0.7735 (mtt-85) REVERT: A 595 LYS cc_start: 0.6747 (ttpt) cc_final: 0.6303 (tppt) outliers start: 11 outliers final: 6 residues processed: 43 average time/residue: 0.2378 time to fit residues: 12.4903 Evaluate side-chains 43 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 34 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 523 ARG Chi-restraints excluded: chain A residue 569 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 46 optimal weight: 0.0870 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 0.0020 chunk 27 optimal weight: 0.0970 chunk 19 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 13 optimal weight: 0.3980 overall best weight: 0.2364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 1 ASN A 533 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4140 Z= 0.258 Angle : 0.543 6.541 5616 Z= 0.276 Chirality : 0.042 0.169 593 Planarity : 0.004 0.032 741 Dihedral : 5.418 78.951 567 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.35 % Allowed : 10.80 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.39), residues: 493 helix: 1.71 (0.45), residues: 139 sheet: 1.01 (0.58), residues: 86 loop : -0.24 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 592 HIS 0.004 0.001 HIS A 533 PHE 0.017 0.002 PHE A 128 TYR 0.013 0.002 TYR A 102 ARG 0.003 0.000 ARG A 549 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 35 time to evaluate : 0.462 Fit side-chains REVERT: A 1 ASN cc_start: 0.6335 (t0) cc_final: 0.6097 (t0) REVERT: A 116 ARG cc_start: 0.7217 (ttp-110) cc_final: 0.6765 (mtm180) REVERT: A 166 GLU cc_start: 0.7350 (tp30) cc_final: 0.6896 (tt0) REVERT: A 169 ASN cc_start: 0.7118 (m-40) cc_final: 0.6767 (m-40) REVERT: A 170 GLN cc_start: 0.7099 (mm-40) cc_final: 0.6820 (mt0) REVERT: A 424 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7114 (tt0) REVERT: A 459 MET cc_start: 0.8572 (mtm) cc_final: 0.8334 (mtm) REVERT: A 496 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7899 (tm-30) REVERT: A 523 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8587 (mtm-85) REVERT: A 549 ARG cc_start: 0.8200 (mtm-85) cc_final: 0.7736 (mtt-85) REVERT: A 595 LYS cc_start: 0.6749 (ttpt) cc_final: 0.6250 (tppt) outliers start: 10 outliers final: 5 residues processed: 43 average time/residue: 0.2226 time to fit residues: 11.7290 Evaluate side-chains 41 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 33 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 523 ARG Chi-restraints excluded: chain A residue 569 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.5980 chunk 42 optimal weight: 0.4980 chunk 44 optimal weight: 0.0030 chunk 29 optimal weight: 0.7980 chunk 47 optimal weight: 0.0980 chunk 28 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 45 optimal weight: 0.3980 chunk 39 optimal weight: 0.4980 overall best weight: 0.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4140 Z= 0.317 Angle : 0.563 5.603 5616 Z= 0.289 Chirality : 0.043 0.177 593 Planarity : 0.004 0.033 741 Dihedral : 5.601 81.970 567 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.11 % Allowed : 11.03 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.40), residues: 493 helix: 1.62 (0.45), residues: 139 sheet: 0.86 (0.58), residues: 90 loop : -0.21 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 592 HIS 0.003 0.001 HIS A 533 PHE 0.018 0.002 PHE A 128 TYR 0.016 0.002 TYR A 102 ARG 0.003 0.000 ARG A 601 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 32 time to evaluate : 0.422 Fit side-chains REVERT: A 128 PHE cc_start: 0.8682 (p90) cc_final: 0.8303 (p90) REVERT: A 130 MET cc_start: 0.7883 (tpt) cc_final: 0.7668 (tpt) REVERT: A 166 GLU cc_start: 0.7368 (tp30) cc_final: 0.6914 (tt0) REVERT: A 169 ASN cc_start: 0.7121 (m-40) cc_final: 0.6766 (m-40) REVERT: A 170 GLN cc_start: 0.7091 (mm-40) cc_final: 0.6826 (mt0) REVERT: A 424 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7095 (tt0) REVERT: A 459 MET cc_start: 0.8600 (mtm) cc_final: 0.8363 (mtm) REVERT: A 496 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7978 (tm-30) REVERT: A 523 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8570 (mtm-85) REVERT: A 549 ARG cc_start: 0.8207 (mtm-85) cc_final: 0.7755 (mtt-85) outliers start: 9 outliers final: 5 residues processed: 40 average time/residue: 0.2204 time to fit residues: 10.7718 Evaluate side-chains 40 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 32 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 523 ARG Chi-restraints excluded: chain A residue 569 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 24 optimal weight: 0.0770 chunk 31 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 36 optimal weight: 0.0170 chunk 5 optimal weight: 0.5980 chunk 11 optimal weight: 0.3980 chunk 39 optimal weight: 0.9990 chunk 16 optimal weight: 0.3980 overall best weight: 0.2976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 1 ASN A 533 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4140 Z= 0.313 Angle : 0.568 5.608 5616 Z= 0.292 Chirality : 0.043 0.174 593 Planarity : 0.004 0.034 741 Dihedral : 5.674 84.182 567 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.11 % Allowed : 11.27 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.39), residues: 493 helix: 1.59 (0.45), residues: 139 sheet: 0.86 (0.58), residues: 90 loop : -0.22 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 592 HIS 0.003 0.001 HIS A 533 PHE 0.018 0.002 PHE A 128 TYR 0.016 0.002 TYR A 102 ARG 0.003 0.000 ARG A 601 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 34 time to evaluate : 0.461 Fit side-chains REVERT: A 116 ARG cc_start: 0.7124 (ttp-110) cc_final: 0.6703 (mtm180) REVERT: A 128 PHE cc_start: 0.8684 (p90) cc_final: 0.8290 (p90) REVERT: A 166 GLU cc_start: 0.7374 (tp30) cc_final: 0.6919 (tt0) REVERT: A 169 ASN cc_start: 0.7147 (m-40) cc_final: 0.6668 (m-40) REVERT: A 170 GLN cc_start: 0.7060 (mm-40) cc_final: 0.6843 (mt0) REVERT: A 424 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7093 (tt0) REVERT: A 459 MET cc_start: 0.8596 (mtm) cc_final: 0.8363 (mtm) REVERT: A 496 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7997 (tm-30) REVERT: A 523 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8590 (mtm-85) REVERT: A 549 ARG cc_start: 0.8198 (mtm-85) cc_final: 0.7736 (mtt-85) outliers start: 9 outliers final: 6 residues processed: 42 average time/residue: 0.2160 time to fit residues: 11.2015 Evaluate side-chains 40 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 31 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 523 ARG Chi-restraints excluded: chain A residue 569 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.0980 chunk 5 optimal weight: 0.6980 chunk 7 optimal weight: 0.1980 chunk 34 optimal weight: 0.7980 chunk 2 optimal weight: 0.4980 chunk 28 optimal weight: 0.3980 chunk 45 optimal weight: 0.1980 chunk 26 optimal weight: 0.0670 chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 0.0870 chunk 30 optimal weight: 0.4980 overall best weight: 0.1296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.110667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.096489 restraints weight = 5410.652| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.83 r_work: 0.3023 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4140 Z= 0.181 Angle : 0.513 5.306 5616 Z= 0.262 Chirality : 0.041 0.155 593 Planarity : 0.004 0.034 741 Dihedral : 5.367 81.260 567 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.64 % Allowed : 11.97 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.39), residues: 493 helix: 1.83 (0.45), residues: 138 sheet: 0.96 (0.58), residues: 86 loop : -0.24 (0.40), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 592 HIS 0.005 0.001 HIS A 533 PHE 0.015 0.001 PHE A 128 TYR 0.009 0.001 TYR A 157 ARG 0.003 0.000 ARG A 601 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1495.27 seconds wall clock time: 28 minutes 14.95 seconds (1694.95 seconds total)