Starting phenix.real_space_refine on Mon Jan 13 21:19:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v3q_42950/01_2025/8v3q_42950.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v3q_42950/01_2025/8v3q_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_42950/01_2025/8v3q_42950.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v3q_42950/01_2025/8v3q_42950.map" model { file = "/net/cci-nas-00/data/ceres_data/8v3q_42950/01_2025/8v3q_42950.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v3q_42950/01_2025/8v3q_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-5571/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: 5.21, per 1000 atoms: 1.29 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: 0.95 Conformation dependent library (CDL) restraints added in 551.4 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: 1.07 Time building geometry restraints manager: 1.14 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: 6.480 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.900 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.730 ------------------------------------------------------------------------------- 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 : 0.516 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: 0.2481 time to fit residues: 19.2819 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 : 0.445 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.110040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.096972 restraints weight = 5559.170| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.71 r_work: 0.3005 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 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 : 0.458 Fit side-chains REVERT: A 133 THR cc_start: 0.7965 (p) cc_final: 0.7725 (t) REVERT: A 166 GLU cc_start: 0.7991 (tp30) cc_final: 0.7595 (tt0) REVERT: A 169 ASN cc_start: 0.7966 (m-40) cc_final: 0.7672 (m-40) REVERT: A 190 TYR cc_start: 0.8677 (t80) cc_final: 0.8301 (t80) REVERT: A 424 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7361 (tt0) REVERT: A 595 LYS cc_start: 0.7634 (ttpt) cc_final: 0.6668 (mttt) outliers start: 6 outliers final: 3 residues processed: 59 average time/residue: 0.2073 time to fit residues: 14.9217 Evaluate side-chains 40 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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 12 optimal weight: 0.9990 chunk 42 optimal weight: 0.0570 chunk 40 optimal weight: 0.3980 chunk 47 optimal weight: 0.4980 chunk 34 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 37 optimal weight: 0.2980 chunk 10 optimal weight: 0.0770 chunk 14 optimal weight: 0.0980 overall best weight: 0.1856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS A 533 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.107584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.094172 restraints weight = 5698.114| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.77 r_work: 0.2952 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2066 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= 0.235 Angle : 0.547 5.228 5616 Z= 0.282 Chirality : 0.042 0.157 593 Planarity : 0.004 0.037 741 Dihedral : 5.423 73.352 567 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.88 % Allowed : 11.03 % Favored : 87.09 % 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 (0.44), residues: 140 sheet: 0.80 (0.57), residues: 92 loop : -0.28 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 592 HIS 0.005 0.001 HIS A 533 PHE 0.010 0.001 PHE A 284 TYR 0.014 0.002 TYR A 102 ARG 0.005 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 51 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.472 Fit side-chains REVERT: A 166 GLU cc_start: 0.8059 (tp30) cc_final: 0.7643 (tt0) REVERT: A 169 ASN cc_start: 0.7907 (m-40) cc_final: 0.7681 (m-40) REVERT: A 424 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7331 (tt0) REVERT: A 595 LYS cc_start: 0.7717 (ttpt) cc_final: 0.6828 (mttt) REVERT: A 601 ARG cc_start: 0.6755 (ptp-170) cc_final: 0.6461 (ptp-170) outliers start: 8 outliers final: 4 residues processed: 50 average time/residue: 0.1893 time to fit residues: 11.9773 Evaluate side-chains 46 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 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 30 optimal weight: 0.9980 chunk 29 optimal weight: 0.1980 chunk 6 optimal weight: 0.0770 chunk 39 optimal weight: 0.9980 chunk 46 optimal weight: 0.1980 chunk 38 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 0.0970 chunk 43 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 overall best weight: 0.2136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.105583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.092266 restraints weight = 5746.532| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.79 r_work: 0.2924 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4140 Z= 0.240 Angle : 0.534 5.251 5616 Z= 0.274 Chirality : 0.042 0.157 593 Planarity : 0.004 0.035 741 Dihedral : 5.407 74.207 567 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.58 % Allowed : 10.56 % 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: 0.64 (0.39), residues: 493 helix: 1.43 (0.45), residues: 140 sheet: 0.79 (0.57), residues: 92 loop : -0.22 (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 0.010 0.002 PHE A 128 TYR 0.014 0.002 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 51 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.466 Fit side-chains REVERT: A 166 GLU cc_start: 0.8064 (tp30) cc_final: 0.7639 (tt0) REVERT: A 169 ASN cc_start: 0.7897 (m-40) cc_final: 0.7662 (m-40) REVERT: A 424 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7415 (tt0) REVERT: A 459 MET cc_start: 0.9236 (mtm) cc_final: 0.9028 (mtm) REVERT: A 496 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8408 (tm-30) REVERT: A 595 LYS cc_start: 0.7785 (ttpt) cc_final: 0.7456 (tppt) outliers start: 11 outliers final: 5 residues processed: 49 average time/residue: 0.2188 time to fit residues: 13.1671 Evaluate side-chains 46 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.450 ------------------------------------------------------------------------------- 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 569 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.2980 chunk 44 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 39 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 chunk 25 optimal weight: 0.0970 chunk 23 optimal weight: 0.0670 chunk 28 optimal weight: 0.3980 overall best weight: 0.2516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.103225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.089835 restraints weight = 5818.605| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.77 r_work: 0.2898 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4140 Z= 0.274 Angle : 0.546 5.376 5616 Z= 0.280 Chirality : 0.042 0.165 593 Planarity : 0.004 0.032 741 Dihedral : 5.447 75.259 567 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.58 % Allowed : 11.03 % 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: 0.72 (0.39), residues: 493 helix: 1.52 (0.45), residues: 140 sheet: 1.24 (0.61), residues: 82 loop : -0.29 (0.39), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 592 HIS 0.004 0.001 HIS A 336 PHE 0.013 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 to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.467 Fit side-chains REVERT: A 116 ARG cc_start: 0.8023 (ttp-110) cc_final: 0.7465 (mtm180) REVERT: A 166 GLU cc_start: 0.8123 (tp30) cc_final: 0.7720 (tt0) REVERT: A 169 ASN cc_start: 0.7886 (m-40) cc_final: 0.7675 (m-40) REVERT: A 424 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7367 (tt0) REVERT: A 459 MET cc_start: 0.9224 (mtm) cc_final: 0.9017 (mtm) REVERT: A 549 ARG cc_start: 0.8464 (mtm-85) cc_final: 0.8095 (mtt-85) REVERT: A 595 LYS cc_start: 0.7842 (ttpt) cc_final: 0.7397 (tppt) outliers start: 11 outliers final: 7 residues processed: 50 average time/residue: 0.2091 time to fit residues: 12.7930 Evaluate side-chains 46 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 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 569 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 29 optimal weight: 0.8980 chunk 26 optimal weight: 0.0870 chunk 38 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 8 optimal weight: 0.4980 chunk 14 optimal weight: 0.0870 chunk 44 optimal weight: 0.7980 chunk 18 optimal weight: 0.2980 chunk 41 optimal weight: 0.0770 chunk 13 optimal weight: 0.0770 chunk 1 optimal weight: 0.1980 overall best weight: 0.1052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 1 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.112302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.098161 restraints weight = 5520.635| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.85 r_work: 0.3026 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2689 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= 0.159 Angle : 0.506 5.415 5616 Z= 0.257 Chirality : 0.040 0.151 593 Planarity : 0.004 0.032 741 Dihedral : 5.212 74.765 567 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.58 % Allowed : 11.74 % 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: 0.77 (0.40), residues: 493 helix: 1.77 (0.45), residues: 140 sheet: 0.52 (0.54), residues: 98 loop : -0.15 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 592 HIS 0.003 0.001 HIS A 533 PHE 0.014 0.001 PHE A 128 TYR 0.008 0.001 TYR A 157 ARG 0.003 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 55 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.549 Fit side-chains REVERT: A 1 ASN cc_start: 0.7271 (OUTLIER) cc_final: 0.7016 (t0) REVERT: A 116 ARG cc_start: 0.7982 (ttp-110) cc_final: 0.7554 (mtm180) REVERT: A 166 GLU cc_start: 0.8183 (tp30) cc_final: 0.7821 (tt0) REVERT: A 424 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7425 (tt0) REVERT: A 459 MET cc_start: 0.9133 (mtm) cc_final: 0.8884 (mtm) REVERT: A 549 ARG cc_start: 0.8356 (mtm-85) cc_final: 0.7999 (mtt-85) REVERT: A 595 LYS cc_start: 0.7825 (ttpt) cc_final: 0.7549 (tppt) outliers start: 11 outliers final: 5 residues processed: 52 average time/residue: 0.2103 time to fit residues: 13.4723 Evaluate side-chains 45 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 ASN Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 431 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 15 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 25 optimal weight: 0.0970 chunk 26 optimal weight: 0.0870 chunk 1 optimal weight: 0.7980 chunk 11 optimal weight: 0.2980 chunk 45 optimal weight: 0.4980 chunk 46 optimal weight: 0.2980 chunk 33 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 overall best weight: 0.2556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 HIS A 533 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.108265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.094184 restraints weight = 5622.037| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.83 r_work: 0.2986 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4140 Z= 0.277 Angle : 0.558 6.333 5616 Z= 0.285 Chirality : 0.043 0.171 593 Planarity : 0.004 0.031 741 Dihedral : 5.325 74.069 567 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.35 % Allowed : 11.27 % 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: 0.80 (0.40), residues: 493 helix: 1.74 (0.46), residues: 140 sheet: 0.86 (0.58), residues: 88 loop : -0.21 (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 336 PHE 0.015 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 45 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.454 Fit side-chains REVERT: A 116 ARG cc_start: 0.7996 (ttp-110) cc_final: 0.7539 (mtm180) REVERT: A 166 GLU cc_start: 0.8166 (tp30) cc_final: 0.7826 (tt0) REVERT: A 424 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7491 (tt0) REVERT: A 549 ARG cc_start: 0.8409 (mtm-85) cc_final: 0.8044 (mtt-85) REVERT: A 595 LYS cc_start: 0.7820 (ttpt) cc_final: 0.7433 (tppt) outliers start: 10 outliers final: 7 residues processed: 43 average time/residue: 0.1991 time to fit residues: 10.8383 Evaluate side-chains 43 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 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 569 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 16 optimal weight: 0.4980 chunk 6 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 0.0970 chunk 32 optimal weight: 0.4980 chunk 48 optimal weight: 0.3980 chunk 47 optimal weight: 0.0670 chunk 35 optimal weight: 0.5980 chunk 21 optimal weight: 0.2980 overall best weight: 0.2716 ------------------------------------------------------------------------------- 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 = 0.3301 r_free = 0.3301 target = 0.109227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.094850 restraints weight = 5501.244| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.85 r_work: 0.2975 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4140 Z= 0.290 Angle : 0.562 6.428 5616 Z= 0.287 Chirality : 0.043 0.171 593 Planarity : 0.004 0.033 741 Dihedral : 5.446 76.097 567 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.35 % Allowed : 11.50 % Favored : 86.15 % 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: 0.73 (0.39), residues: 493 helix: 1.57 (0.45), residues: 139 sheet: 0.90 (0.58), residues: 88 loop : -0.21 (0.40), residues: 266 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 0.015 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 46 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.480 Fit side-chains REVERT: A 116 ARG cc_start: 0.7975 (ttp-110) cc_final: 0.7497 (mtm180) REVERT: A 166 GLU cc_start: 0.8205 (tp30) cc_final: 0.7846 (tt0) REVERT: A 424 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7525 (tt0) REVERT: A 549 ARG cc_start: 0.8455 (mtm-85) cc_final: 0.8075 (mtt-85) outliers start: 10 outliers final: 8 residues processed: 44 average time/residue: 0.1996 time to fit residues: 11.1470 Evaluate side-chains 44 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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 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 569 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 49 optimal weight: 0.6980 chunk 45 optimal weight: 0.2980 chunk 24 optimal weight: 0.3980 chunk 23 optimal weight: 0.0870 chunk 26 optimal weight: 0.0970 chunk 36 optimal weight: 0.6980 chunk 20 optimal weight: 0.2980 chunk 35 optimal weight: 0.2980 chunk 11 optimal weight: 0.2980 chunk 13 optimal weight: 0.5980 chunk 25 optimal weight: 0.0570 overall best weight: 0.1674 ------------------------------------------------------------------------------- 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 = 0.3314 r_free = 0.3314 target = 0.110170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.095989 restraints weight = 5514.429| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.88 r_work: 0.2995 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2910 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= 0.204 Angle : 0.525 5.354 5616 Z= 0.269 Chirality : 0.041 0.165 593 Planarity : 0.004 0.032 741 Dihedral : 5.327 76.443 567 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.88 % Allowed : 11.97 % Favored : 86.15 % 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: 0.75 (0.39), residues: 493 helix: 1.66 (0.44), residues: 138 sheet: 0.87 (0.58), residues: 88 loop : -0.21 (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 0.020 0.001 PHE A 128 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 44 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.482 Fit side-chains REVERT: A 116 ARG cc_start: 0.7910 (ttp-110) cc_final: 0.7437 (mtm180) REVERT: A 166 GLU cc_start: 0.8156 (tp30) cc_final: 0.7789 (tt0) REVERT: A 424 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7524 (tt0) REVERT: A 549 ARG cc_start: 0.8419 (mtm-85) cc_final: 0.8035 (mtt-85) REVERT: A 595 LYS cc_start: 0.7778 (ttpt) cc_final: 0.7325 (tppt) outliers start: 8 outliers final: 6 residues processed: 43 average time/residue: 0.2096 time to fit residues: 11.2786 Evaluate side-chains 43 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 187 ASP 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 569 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 26 optimal weight: 0.4980 chunk 22 optimal weight: 0.2980 chunk 19 optimal weight: 0.1980 chunk 36 optimal weight: 0.0470 chunk 0 optimal weight: 0.9990 chunk 23 optimal weight: 0.0970 chunk 30 optimal weight: 0.1980 chunk 8 optimal weight: 0.3980 chunk 34 optimal weight: 0.0980 chunk 2 optimal weight: 0.5980 chunk 46 optimal weight: 0.0670 overall best weight: 0.1014 ------------------------------------------------------------------------------- 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 = 0.3343 r_free = 0.3343 target = 0.112338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.097637 restraints weight = 5542.649| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.95 r_work: 0.3019 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4140 Z= 0.160 Angle : 0.505 5.225 5616 Z= 0.258 Chirality : 0.040 0.157 593 Planarity : 0.004 0.032 741 Dihedral : 5.068 73.649 567 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.64 % Allowed : 12.21 % Favored : 86.15 % 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: 1.85 (0.45), residues: 140 sheet: 1.03 (0.61), residues: 81 loop : -0.17 (0.40), residues: 272 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 0.018 0.001 PHE A 128 TYR 0.009 0.001 TYR A 157 ARG 0.003 0.000 ARG A 549 ********************** 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 to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.436 Fit side-chains REVERT: A 116 ARG cc_start: 0.7806 (ttp-110) cc_final: 0.7364 (mtm180) REVERT: A 166 GLU cc_start: 0.8137 (tp30) cc_final: 0.7771 (tt0) REVERT: A 424 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7573 (tt0) REVERT: A 549 ARG cc_start: 0.8363 (mtm-85) cc_final: 0.8113 (mtt-85) REVERT: A 595 LYS cc_start: 0.7726 (ttpt) cc_final: 0.7412 (tppt) outliers start: 7 outliers final: 6 residues processed: 41 average time/residue: 0.1828 time to fit residues: 9.6577 Evaluate side-chains 43 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.775 ------------------------------------------------------------------------------- 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 187 ASP 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 569 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 44 optimal weight: 0.0010 chunk 1 optimal weight: 0.5980 chunk 13 optimal weight: 0.4980 chunk 43 optimal weight: 0.2980 chunk 18 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 0.0870 chunk 30 optimal weight: 0.6980 chunk 29 optimal weight: 0.2980 chunk 38 optimal weight: 0.5980 chunk 32 optimal weight: 0.0040 overall best weight: 0.1376 ------------------------------------------------------------------------------- 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 = 0.3310 r_free = 0.3310 target = 0.110216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.096150 restraints weight = 5492.217| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.83 r_work: 0.3018 rms_B_bonded: 2.32 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: 0.8320 moved from start: 0.2970 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= 0.185 Angle : 0.513 5.278 5616 Z= 0.262 Chirality : 0.041 0.163 593 Planarity : 0.004 0.034 741 Dihedral : 5.021 71.119 567 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.64 % Allowed : 12.44 % Favored : 85.92 % 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: 0.92 (0.40), residues: 493 helix: 1.87 (0.45), residues: 140 sheet: 1.05 (0.61), residues: 81 loop : -0.16 (0.40), residues: 272 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 0.016 0.001 PHE A 128 TYR 0.009 0.001 TYR A 102 ARG 0.002 0.000 ARG A 281 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2453.41 seconds wall clock time: 44 minutes 30.58 seconds (2670.58 seconds total)