Starting phenix.real_space_refine on Fri Dec 27 10:17:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v3q_42950/12_2024/8v3q_42950.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v3q_42950/12_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/cci-nas-00/data/ceres_data/8v3q_42950/12_2024/8v3q_42950.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v3q_42950/12_2024/8v3q_42950.map" model { file = "/net/cci-nas-00/data/ceres_data/8v3q_42950/12_2024/8v3q_42950.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v3q_42950/12_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 "M GLU 5": not complete - not flipped Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 5.10, per 1000 atoms: 1.27 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 457.3 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: 0.44 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: 1.11 Time building geometry restraints manager: 1.12 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: 0.00 - 1.94: 5133 1.94 - 3.88: 369 3.88 - 5.82: 87 5.82 - 7.76: 18 7.76 - 9.70: 9 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: 2.11 - 2.67: 71 2.67 - 3.23: 3511 3.23 - 3.78: 6502 3.78 - 4.34: 8749 4.34 - 4.90: 14577 Nonbonded interactions: 33410 Sorted by model distance: 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=" O HIS A 336 " pdb=" OG SER A 340 " model vdw 2.354 3.040 nonbonded pdb=" OG SER A 581 " pdb=" O HIS A 583 " model vdw 2.399 3.040 ... (remaining 33405 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: 4.080 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: 0.040 Process input model: 16.620 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.970 ------------------------------------------------------------------------------- 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 : 2.109 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 to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.442 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: 0.2501 time to fit residues: 19.4050 Evaluate side-chains 47 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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: 0.1555 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= 0.156 Angle : 0.548 5.158 5616 Z= 0.286 Chirality : 0.041 0.146 593 Planarity : 0.005 0.040 741 Dihedral : 5.669 77.367 567 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 2.68 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: -0.09 (0.37), residues: 493 helix: 0.39 (0.42), residues: 140 sheet: 0.66 (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 0.013 0.001 PHE A 152 TYR 0.009 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 60 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.446 Fit side-chains REVERT: A 13 ARG cc_start: 0.8214 (ttp-170) cc_final: 0.7965 (ttm170) REVERT: A 69 ASN cc_start: 0.7887 (m-40) cc_final: 0.7647 (m-40) REVERT: A 130 MET cc_start: 0.8257 (tpt) cc_final: 0.8036 (tpp) REVERT: A 133 THR cc_start: 0.7773 (p) cc_final: 0.7534 (t) REVERT: A 166 GLU cc_start: 0.7167 (tp30) cc_final: 0.6591 (tt0) REVERT: A 169 ASN cc_start: 0.7214 (m-40) cc_final: 0.6750 (m-40) REVERT: A 170 GLN cc_start: 0.7247 (mm-40) cc_final: 0.6926 (mt0) REVERT: A 190 TYR cc_start: 0.8549 (t80) cc_final: 0.8004 (t80) REVERT: A 424 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7155 (tt0) REVERT: A 595 LYS cc_start: 0.6590 (ttpt) cc_final: 0.5614 (mttt) outliers start: 6 outliers final: 3 residues processed: 59 average time/residue: 0.2090 time to fit residues: 14.9976 Evaluate side-chains 43 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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: 0.0170 chunk 14 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 30 optimal weight: 0.0870 chunk 12 optimal weight: 0.9990 chunk 45 optimal weight: 0.3980 chunk 49 optimal weight: 0.4980 chunk 40 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 36 optimal weight: 0.3980 chunk 44 optimal weight: 0.6980 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS A 336 HIS A 533 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4140 Z= 0.312 Angle : 0.586 5.328 5616 Z= 0.304 Chirality : 0.044 0.165 593 Planarity : 0.005 0.036 741 Dihedral : 5.658 75.430 567 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.82 % Allowed : 9.86 % 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: 0.44 (0.39), residues: 493 helix: 1.09 (0.45), residues: 140 sheet: 0.83 (0.57), residues: 92 loop : -0.30 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 592 HIS 0.004 0.001 HIS A 533 PHE 0.012 0.002 PHE A 245 TYR 0.018 0.002 TYR A 102 ARG 0.005 0.001 ARG A 281 *********************** 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 56 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.508 Fit side-chains REVERT: A 13 ARG cc_start: 0.8224 (ttp-170) cc_final: 0.7887 (ttm170) REVERT: A 128 PHE cc_start: 0.8721 (p90) cc_final: 0.8365 (p90) REVERT: A 166 GLU cc_start: 0.7296 (tp30) cc_final: 0.6771 (tt0) REVERT: A 169 ASN cc_start: 0.7142 (m-40) cc_final: 0.6796 (m-40) REVERT: A 170 GLN cc_start: 0.7224 (mm-40) cc_final: 0.6830 (mt0) REVERT: A 424 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7061 (tt0) REVERT: A 496 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7768 (tm-30) REVERT: A 523 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8623 (mtm-85) REVERT: A 595 LYS cc_start: 0.6739 (ttpt) cc_final: 0.6338 (tppt) outliers start: 12 outliers final: 5 residues processed: 55 average time/residue: 0.2211 time to fit residues: 14.7636 Evaluate side-chains 48 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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 288 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 532 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 0.0980 chunk 23 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 30 optimal weight: 0.1980 chunk 45 optimal weight: 0.3980 chunk 48 optimal weight: 0.0170 chunk 43 optimal weight: 0.0980 chunk 13 optimal weight: 0.0770 chunk 40 optimal weight: 0.0270 chunk 27 optimal weight: 0.1980 overall best weight: 0.0634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4140 Z= 0.134 Angle : 0.494 5.047 5616 Z= 0.254 Chirality : 0.039 0.145 593 Planarity : 0.004 0.034 741 Dihedral : 5.300 76.227 567 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.64 % Allowed : 11.50 % 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: 0.66 (0.39), residues: 493 helix: 1.56 (0.45), residues: 140 sheet: 0.58 (0.55), residues: 98 loop : -0.19 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 592 HIS 0.002 0.001 HIS A 336 PHE 0.009 0.001 PHE A 265 TYR 0.009 0.001 TYR A 157 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 51 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.478 Fit side-chains REVERT: A 13 ARG cc_start: 0.8225 (ttp-170) cc_final: 0.7923 (ttm170) REVERT: A 128 PHE cc_start: 0.8692 (p90) cc_final: 0.8337 (p90) REVERT: A 166 GLU cc_start: 0.7282 (tp30) cc_final: 0.6775 (tt0) REVERT: A 169 ASN cc_start: 0.7135 (m-40) cc_final: 0.6806 (m-40) REVERT: A 170 GLN cc_start: 0.7233 (mm-40) cc_final: 0.6861 (mt0) REVERT: A 424 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7213 (tt0) REVERT: A 459 MET cc_start: 0.8564 (mtm) cc_final: 0.8283 (mtm) REVERT: A 523 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8629 (mtm-85) REVERT: A 595 LYS cc_start: 0.6625 (ttpt) cc_final: 0.6282 (tppt) outliers start: 7 outliers final: 4 residues processed: 49 average time/residue: 0.2205 time to fit residues: 13.1126 Evaluate side-chains 48 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ASP 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 523 ARG 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: 0.0980 chunk 41 optimal weight: 0.5980 chunk 33 optimal weight: 0.0970 chunk 24 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 310 ASN A 533 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 4140 Z= 0.425 Angle : 0.609 5.602 5616 Z= 0.315 Chirality : 0.045 0.173 593 Planarity : 0.005 0.030 741 Dihedral : 5.709 78.275 567 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.05 % Allowed : 11.74 % Favored : 85.21 % 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: 0.68 (0.39), residues: 493 helix: 1.37 (0.46), residues: 141 sheet: 1.28 (0.61), residues: 82 loop : -0.28 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 592 HIS 0.004 0.001 HIS A 214 PHE 0.012 0.002 PHE A 143 TYR 0.021 0.002 TYR A 102 ARG 0.004 0.001 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 51 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.445 Fit side-chains REVERT: A 128 PHE cc_start: 0.8764 (p90) cc_final: 0.8402 (p90) REVERT: A 166 GLU cc_start: 0.7340 (tp30) cc_final: 0.6834 (tt0) REVERT: A 169 ASN cc_start: 0.7145 (m-40) cc_final: 0.6666 (m-40) REVERT: A 170 GLN cc_start: 0.7053 (mm-40) cc_final: 0.6705 (mt0) REVERT: A 424 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7126 (tt0) REVERT: A 496 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7713 (tm-30) REVERT: A 523 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8593 (mtm-85) REVERT: A 549 ARG cc_start: 0.8143 (mtm-85) cc_final: 0.7699 (mtt-85) outliers start: 13 outliers final: 8 residues processed: 50 average time/residue: 0.2036 time to fit residues: 12.6116 Evaluate side-chains 46 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 133 THR Chi-restraints excluded: chain A residue 187 ASP 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 0.1980 chunk 48 optimal weight: 0.2980 chunk 40 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 0.2980 chunk 25 optimal weight: 0.0770 chunk 46 optimal weight: 0.0980 chunk 5 optimal weight: 0.4980 chunk 27 optimal weight: 0.0980 chunk 35 optimal weight: 0.0270 overall best weight: 0.0996 ------------------------------------------------------------------------------- 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: 0.7406 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4140 Z= 0.154 Angle : 0.503 5.147 5616 Z= 0.258 Chirality : 0.040 0.146 593 Planarity : 0.004 0.032 741 Dihedral : 5.399 79.793 567 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.64 % Allowed : 13.38 % Favored : 84.98 % 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: 0.81 (0.40), residues: 493 helix: 1.68 (0.45), residues: 140 sheet: 0.94 (0.59), residues: 88 loop : -0.18 (0.40), residues: 265 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 0.009 0.001 PHE A 265 TYR 0.009 0.001 TYR A 157 ARG 0.004 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 49 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.486 Fit side-chains REVERT: A 116 ARG cc_start: 0.7409 (ttp-110) cc_final: 0.6944 (mtm180) REVERT: A 128 PHE cc_start: 0.8735 (p90) cc_final: 0.8311 (p90) REVERT: A 166 GLU cc_start: 0.7353 (tp30) cc_final: 0.6874 (tt0) REVERT: A 169 ASN cc_start: 0.7117 (m-40) cc_final: 0.6758 (m-40) REVERT: A 170 GLN cc_start: 0.7108 (mm-40) cc_final: 0.6776 (mt0) REVERT: A 424 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7158 (tt0) REVERT: A 459 MET cc_start: 0.8513 (mtm) cc_final: 0.8214 (mtm) REVERT: A 523 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8649 (mtm-85) REVERT: A 549 ARG cc_start: 0.8149 (mtm-85) cc_final: 0.7705 (mtt-85) REVERT: A 595 LYS cc_start: 0.6738 (ttpt) cc_final: 0.6226 (tppt) outliers start: 7 outliers final: 4 residues processed: 46 average time/residue: 0.2242 time to fit residues: 12.6509 Evaluate side-chains 44 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 523 ARG Chi-restraints excluded: chain A residue 569 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.0870 chunk 40 optimal weight: 0.3980 chunk 48 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 29 optimal weight: 0.3980 chunk 22 optimal weight: 0.8980 chunk 19 optimal weight: 0.0370 chunk 28 optimal weight: 0.3980 chunk 14 optimal weight: 0.4980 chunk 9 optimal weight: 0.1980 chunk 32 optimal weight: 0.0370 overall best weight: 0.1514 ------------------------------------------------------------------------------- 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: 0.7414 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4140 Z= 0.196 Angle : 0.522 5.281 5616 Z= 0.266 Chirality : 0.041 0.163 593 Planarity : 0.004 0.032 741 Dihedral : 5.319 78.534 567 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.35 % Allowed : 12.68 % Favored : 84.98 % 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: 0.83 (0.40), residues: 493 helix: 1.78 (0.45), residues: 140 sheet: 0.82 (0.58), residues: 88 loop : -0.17 (0.40), residues: 265 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 0.009 0.001 PHE A 265 TYR 0.010 0.001 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 50 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.503 Fit side-chains REVERT: A 13 ARG cc_start: 0.8226 (ttp-170) cc_final: 0.7958 (ttm170) REVERT: A 116 ARG cc_start: 0.7301 (ttp-110) cc_final: 0.6834 (mtm180) REVERT: A 128 PHE cc_start: 0.8737 (p90) cc_final: 0.8307 (p90) REVERT: A 166 GLU cc_start: 0.7340 (tp30) cc_final: 0.6882 (tt0) REVERT: A 169 ASN cc_start: 0.7111 (m-40) cc_final: 0.6771 (m-40) REVERT: A 170 GLN cc_start: 0.7106 (mm-40) cc_final: 0.6816 (mt0) REVERT: A 424 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7149 (tt0) REVERT: A 459 MET cc_start: 0.8490 (mtm) cc_final: 0.8199 (mtm) REVERT: A 496 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8058 (tm-30) REVERT: A 523 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8580 (mtm-85) REVERT: A 549 ARG cc_start: 0.8142 (mtm-85) cc_final: 0.7698 (mtt-85) REVERT: A 595 LYS cc_start: 0.6743 (ttpt) cc_final: 0.6229 (tppt) outliers start: 10 outliers final: 5 residues processed: 48 average time/residue: 0.2579 time to fit residues: 14.8408 Evaluate side-chains 45 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 0.4980 chunk 4 optimal weight: 0.9980 chunk 37 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 chunk 46 optimal weight: 0.0770 chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 0.0670 chunk 19 optimal weight: 0.0050 chunk 35 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 overall best weight: 0.2290 ------------------------------------------------------------------------------- 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: 0.7431 moved from start: 0.2789 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= 0.254 Angle : 0.552 6.550 5616 Z= 0.281 Chirality : 0.042 0.169 593 Planarity : 0.004 0.033 741 Dihedral : 5.431 79.300 567 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.58 % Allowed : 12.21 % Favored : 85.21 % 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: 0.84 (0.40), residues: 493 helix: 1.75 (0.45), residues: 141 sheet: 0.85 (0.58), residues: 88 loop : -0.15 (0.41), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 592 HIS 0.004 0.001 HIS A 533 PHE 0.008 0.001 PHE A 239 TYR 0.013 0.001 TYR A 102 ARG 0.003 0.000 ARG A 281 *********************** 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 48 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.459 Fit side-chains REVERT: A 116 ARG cc_start: 0.7266 (ttp-110) cc_final: 0.6794 (mtm180) REVERT: A 128 PHE cc_start: 0.8739 (p90) cc_final: 0.8340 (p90) REVERT: A 166 GLU cc_start: 0.7356 (tp30) cc_final: 0.6900 (tt0) REVERT: A 169 ASN cc_start: 0.7124 (m-40) cc_final: 0.6783 (m-40) REVERT: A 170 GLN cc_start: 0.7103 (mm-40) cc_final: 0.6822 (mt0) REVERT: A 424 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7118 (tt0) REVERT: A 459 MET cc_start: 0.8495 (mtm) cc_final: 0.8218 (mtm) REVERT: A 496 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7960 (tm-30) REVERT: A 523 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8591 (mtm-85) REVERT: A 549 ARG cc_start: 0.8183 (mtm-85) cc_final: 0.7739 (mtt-85) outliers start: 11 outliers final: 7 residues processed: 45 average time/residue: 0.2293 time to fit residues: 12.6647 Evaluate side-chains 45 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 187 ASP 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: 0.1980 chunk 42 optimal weight: 0.1980 chunk 44 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 47 optimal weight: 0.0270 chunk 28 optimal weight: 0.3980 chunk 22 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 49 optimal weight: 0.0570 chunk 45 optimal weight: 0.2980 chunk 39 optimal weight: 0.7980 overall best weight: 0.1556 ------------------------------------------------------------------------------- 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: 0.7418 moved from start: 0.2816 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= 0.196 Angle : 0.518 5.327 5616 Z= 0.265 Chirality : 0.041 0.164 593 Planarity : 0.004 0.033 741 Dihedral : 5.324 79.473 567 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.11 % Allowed : 12.91 % Favored : 84.98 % 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 (0.40), residues: 493 helix: 1.84 (0.45), residues: 140 sheet: 0.84 (0.58), 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 0.009 0.001 PHE A 265 TYR 0.010 0.001 TYR A 102 ARG 0.003 0.000 ARG A 549 *********************** 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 46 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.511 Fit side-chains REVERT: A 116 ARG cc_start: 0.7203 (ttp-110) cc_final: 0.6736 (mtm180) REVERT: A 128 PHE cc_start: 0.8744 (p90) cc_final: 0.8322 (p90) REVERT: A 166 GLU cc_start: 0.7345 (tp30) cc_final: 0.6889 (tt0) REVERT: A 169 ASN cc_start: 0.7123 (m-40) cc_final: 0.6773 (m-40) REVERT: A 170 GLN cc_start: 0.7082 (mm-40) cc_final: 0.6815 (mt0) REVERT: A 424 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7137 (tt0) REVERT: A 459 MET cc_start: 0.8577 (mtm) cc_final: 0.8284 (mtm) REVERT: A 523 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8589 (mtm-85) REVERT: A 549 ARG cc_start: 0.8176 (mtm-85) cc_final: 0.7734 (mtt-85) REVERT: A 595 LYS cc_start: 0.6751 (ttpt) cc_final: 0.6254 (tppt) outliers start: 9 outliers final: 7 residues processed: 44 average time/residue: 0.2215 time to fit residues: 11.9090 Evaluate side-chains 47 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 187 ASP 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 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: 0.9980 chunk 30 optimal weight: 0.0770 chunk 24 optimal weight: 0.4980 chunk 31 optimal weight: 0.4980 chunk 42 optimal weight: 0.0050 chunk 12 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 11 optimal weight: 0.0570 chunk 39 optimal weight: 0.9990 chunk 16 optimal weight: 0.1980 overall best weight: 0.1670 ------------------------------------------------------------------------------- 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: 0.7420 moved from start: 0.2875 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= 0.207 Angle : 0.524 5.369 5616 Z= 0.268 Chirality : 0.041 0.164 593 Planarity : 0.004 0.033 741 Dihedral : 5.284 78.402 567 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.82 % Allowed : 11.74 % Favored : 85.45 % 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: 0.85 (0.40), residues: 493 helix: 1.84 (0.45), residues: 138 sheet: 0.87 (0.59), residues: 88 loop : -0.19 (0.40), residues: 267 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 0.009 0.001 PHE A 265 TYR 0.011 0.001 TYR A 102 ARG 0.002 0.000 ARG A 281 ********************** 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 50 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.474 Fit side-chains REVERT: A 116 ARG cc_start: 0.7195 (ttp-110) cc_final: 0.6733 (mtm180) REVERT: A 128 PHE cc_start: 0.8755 (p90) cc_final: 0.8345 (p90) REVERT: A 166 GLU cc_start: 0.7347 (tp30) cc_final: 0.6894 (tt0) REVERT: A 169 ASN cc_start: 0.7123 (m-40) cc_final: 0.6781 (m-40) REVERT: A 170 GLN cc_start: 0.7041 (mm-40) cc_final: 0.6831 (mt0) REVERT: A 424 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7142 (tt0) REVERT: A 459 MET cc_start: 0.8555 (mtm) cc_final: 0.8285 (mtm) REVERT: A 523 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8584 (mtm-85) REVERT: A 549 ARG cc_start: 0.8181 (mtm-85) cc_final: 0.7739 (mtt-85) REVERT: A 595 LYS cc_start: 0.6746 (ttpt) cc_final: 0.6254 (tppt) outliers start: 12 outliers final: 8 residues processed: 46 average time/residue: 0.2266 time to fit residues: 12.7342 Evaluate side-chains 47 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 133 THR Chi-restraints excluded: chain A residue 187 ASP 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 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: 0.5980 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 chunk 34 optimal weight: 0.7980 chunk 2 optimal weight: 0.0980 chunk 28 optimal weight: 0.3980 chunk 45 optimal weight: 0.6980 chunk 26 optimal weight: 0.0010 chunk 1 optimal weight: 0.0060 chunk 31 optimal weight: 0.0770 chunk 30 optimal weight: 0.0980 overall best weight: 0.0560 ------------------------------------------------------------------------------- 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 = 0.3344 r_free = 0.3344 target = 0.112434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.098490 restraints weight = 5442.402| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.84 r_work: 0.3056 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4140 Z= 0.138 Angle : 0.497 5.163 5616 Z= 0.254 Chirality : 0.039 0.150 593 Planarity : 0.004 0.035 741 Dihedral : 4.974 74.826 567 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.35 % Allowed : 11.97 % Favored : 85.68 % 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: 0.89 (0.40), residues: 493 helix: 2.01 (0.45), residues: 140 sheet: 0.44 (0.55), residues: 98 loop : -0.10 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 592 HIS 0.004 0.001 HIS A 533 PHE 0.009 0.001 PHE A 265 TYR 0.009 0.001 TYR A 157 ARG 0.003 0.000 ARG A 549 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1608.88 seconds wall clock time: 29 minutes 40.22 seconds (1780.22 seconds total)