Starting phenix.real_space_refine on Wed Jul 23 19:08:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v3q_42950/07_2025/8v3q_42950.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v3q_42950/07_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_42950/07_2025/8v3q_42950.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v3q_42950/07_2025/8v3q_42950.map" model { file = "/net/cci-nas-00/data/ceres_data/8v3q_42950/07_2025/8v3q_42950.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v3q_42950/07_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-5711/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: 5.67, per 1000 atoms: 1.41 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: 1.00 Conformation dependent library (CDL) restraints added in 489.1 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: 0.46 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: 1.29 Time building geometry restraints manager: 1.22 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: 4.570 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: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 18.380 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.320 ------------------------------------------------------------------------------- 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 4143 Z= 0.407 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 Details of bonding type rmsd hydrogen bonds : bond 0.17391 ( 151) hydrogen bonds : angle 7.79596 ( 426) metal coordination : bond 0.01221 ( 2) covalent geometry : bond 0.00928 ( 4140) covalent geometry : angle 1.22271 ( 5616) Misc. bond : bond 0.06001 ( 1) *********************** 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 : 0.466 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: 0.2402 time to fit residues: 18.7500 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 : 0.467 ------------------------------------------------------------------------------- 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: 0.0770 chunk 29 optimal weight: 0.0980 chunk 45 optimal weight: 0.3980 overall best weight: 0.0714 ------------------------------------------------------------------------------- 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 = 0.3273 r_free = 0.3273 target = 0.110600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.098017 restraints weight = 5589.641| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.62 r_work: 0.3015 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4143 Z= 0.107 Angle : 0.546 5.063 5616 Z= 0.285 Chirality : 0.041 0.151 593 Planarity : 0.005 0.040 741 Dihedral : 5.689 78.329 567 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.41 % Allowed : 9.86 % Favored : 88.73 % 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: -0.06 (0.37), residues: 493 helix: 0.40 (0.42), residues: 140 sheet: 0.66 (0.56), residues: 90 loop : -0.48 (0.38), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 592 HIS 0.009 0.001 HIS A 533 PHE 0.013 0.001 PHE A 152 TYR 0.008 0.001 TYR A 102 ARG 0.005 0.000 ARG A 549 Details of bonding type rmsd hydrogen bonds : bond 0.03882 ( 151) hydrogen bonds : angle 5.46824 ( 426) metal coordination : bond 0.00155 ( 2) covalent geometry : bond 0.00241 ( 4140) covalent geometry : angle 0.54635 ( 5616) Misc. bond : bond 0.00061 ( 1) *********************** 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 : 0.659 Fit side-chains REVERT: A 133 THR cc_start: 0.7943 (p) cc_final: 0.7712 (t) REVERT: A 166 GLU cc_start: 0.7998 (tp30) cc_final: 0.7590 (tt0) REVERT: A 169 ASN cc_start: 0.7954 (m-40) cc_final: 0.7678 (m-40) REVERT: A 190 TYR cc_start: 0.8668 (t80) cc_final: 0.8313 (t80) REVERT: A 424 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7348 (tt0) REVERT: A 595 LYS cc_start: 0.7680 (ttpt) cc_final: 0.6700 (mttt) outliers start: 6 outliers final: 3 residues processed: 59 average time/residue: 0.2237 time to fit residues: 16.2249 Evaluate side-chains 41 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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: 0.0870 chunk 42 optimal weight: 0.0020 chunk 40 optimal weight: 0.6980 chunk 47 optimal weight: 0.0770 chunk 34 optimal weight: 0.5980 chunk 24 optimal weight: 0.4980 chunk 1 optimal weight: 0.6980 chunk 45 optimal weight: 0.0970 chunk 37 optimal weight: 0.2980 chunk 10 optimal weight: 0.4980 chunk 14 optimal weight: 0.0870 overall best weight: 0.0700 ------------------------------------------------------------------------------- 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 = 0.3285 r_free = 0.3285 target = 0.110923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.097252 restraints weight = 5640.802| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.79 r_work: 0.3007 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4143 Z= 0.100 Angle : 0.508 5.272 5616 Z= 0.262 Chirality : 0.040 0.146 593 Planarity : 0.004 0.036 741 Dihedral : 5.288 74.183 567 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.94 % Allowed : 11.97 % 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: 0.43 (0.39), residues: 493 helix: 1.07 (0.44), residues: 140 sheet: 0.62 (0.55), residues: 98 loop : -0.23 (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 0.008 0.001 TYR A 157 ARG 0.005 0.000 ARG A 281 Details of bonding type rmsd hydrogen bonds : bond 0.03337 ( 151) hydrogen bonds : angle 5.07178 ( 426) metal coordination : bond 0.00119 ( 2) covalent geometry : bond 0.00226 ( 4140) covalent geometry : angle 0.50801 ( 5616) Misc. bond : bond 0.00036 ( 1) *********************** 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 47 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 1.110 Fit side-chains REVERT: A 166 GLU cc_start: 0.7968 (tp30) cc_final: 0.7593 (tt0) REVERT: A 169 ASN cc_start: 0.7917 (m-40) cc_final: 0.7639 (m-40) REVERT: A 190 TYR cc_start: 0.8771 (t80) cc_final: 0.8382 (t80) REVERT: A 424 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7356 (tt0) REVERT: A 459 MET cc_start: 0.9164 (mtm) cc_final: 0.8909 (mtm) REVERT: A 595 LYS cc_start: 0.7618 (ttpt) cc_final: 0.6747 (mttt) outliers start: 4 outliers final: 1 residues processed: 46 average time/residue: 0.2122 time to fit residues: 12.3992 Evaluate side-chains 41 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 431 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 30 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 38 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 4 optimal weight: 0.2980 chunk 8 optimal weight: 0.4980 chunk 43 optimal weight: 0.0870 chunk 9 optimal weight: 0.4980 overall best weight: 0.3758 ------------------------------------------------------------------------------- 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 = 0.3175 r_free = 0.3175 target = 0.102756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.089405 restraints weight = 5766.659| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.76 r_work: 0.2893 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 4143 Z= 0.242 Angle : 0.616 5.564 5616 Z= 0.318 Chirality : 0.045 0.173 593 Planarity : 0.005 0.031 741 Dihedral : 5.644 73.912 567 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.82 % Allowed : 10.33 % 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: 1.24 (0.45), residues: 140 sheet: 1.33 (0.62), residues: 82 loop : -0.26 (0.38), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 592 HIS 0.005 0.001 HIS A 336 PHE 0.012 0.002 PHE A 245 TYR 0.021 0.002 TYR A 102 ARG 0.005 0.001 ARG A 549 Details of bonding type rmsd hydrogen bonds : bond 0.04359 ( 151) hydrogen bonds : angle 5.24969 ( 426) metal coordination : bond 0.00598 ( 2) covalent geometry : bond 0.00595 ( 4140) covalent geometry : angle 0.61587 ( 5616) Misc. bond : bond 0.00122 ( 1) *********************** 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 50 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.459 Fit side-chains REVERT: A 128 PHE cc_start: 0.8841 (p90) cc_final: 0.8494 (p90) REVERT: A 166 GLU cc_start: 0.8116 (tp30) cc_final: 0.7678 (tt0) REVERT: A 169 ASN cc_start: 0.7955 (m-40) cc_final: 0.7708 (m-40) REVERT: A 424 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7361 (tt0) REVERT: A 496 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8436 (tm-30) REVERT: A 595 LYS cc_start: 0.7832 (ttpt) cc_final: 0.7419 (tppt) outliers start: 12 outliers final: 7 residues processed: 50 average time/residue: 0.2085 time to fit residues: 12.8666 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 : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 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 532 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.4980 chunk 44 optimal weight: 0.7980 chunk 45 optimal weight: 0.2980 chunk 39 optimal weight: 0.9990 chunk 16 optimal weight: 0.0870 chunk 13 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 0.1980 chunk 25 optimal weight: 0.0770 chunk 23 optimal weight: 0.1980 chunk 28 optimal weight: 0.4980 overall best weight: 0.1716 ------------------------------------------------------------------------------- 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 = 0.3197 r_free = 0.3197 target = 0.104599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.091233 restraints weight = 5782.746| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.77 r_work: 0.2920 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4143 Z= 0.131 Angle : 0.524 5.239 5616 Z= 0.269 Chirality : 0.041 0.156 593 Planarity : 0.004 0.032 741 Dihedral : 5.443 76.543 567 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.88 % Allowed : 11.50 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.39), residues: 493 helix: 1.51 (0.45), residues: 140 sheet: 1.06 (0.59), residues: 88 loop : -0.24 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 592 HIS 0.002 0.001 HIS A 533 PHE 0.009 0.001 PHE A 265 TYR 0.012 0.001 TYR A 102 ARG 0.003 0.000 ARG A 549 Details of bonding type rmsd hydrogen bonds : bond 0.03489 ( 151) hydrogen bonds : angle 4.99991 ( 426) metal coordination : bond 0.00283 ( 2) covalent geometry : bond 0.00319 ( 4140) covalent geometry : angle 0.52356 ( 5616) Misc. bond : bond 0.00058 ( 1) *********************** 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 48 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.511 Fit side-chains REVERT: A 116 ARG cc_start: 0.8081 (ttp-110) cc_final: 0.7608 (mtm180) REVERT: A 128 PHE cc_start: 0.8823 (p90) cc_final: 0.8478 (p90) REVERT: A 166 GLU cc_start: 0.8072 (tp30) cc_final: 0.7636 (tt0) REVERT: A 169 ASN cc_start: 0.7872 (m-40) cc_final: 0.7644 (m-40) REVERT: A 424 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7409 (tt0) REVERT: A 459 MET cc_start: 0.9226 (mtm) cc_final: 0.8999 (mtm) REVERT: A 496 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8419 (tm-30) REVERT: A 595 LYS cc_start: 0.7754 (ttpt) cc_final: 0.7332 (tppt) REVERT: A 601 ARG cc_start: 0.6778 (ptp-170) cc_final: 0.6431 (mtp-110) outliers start: 8 outliers final: 4 residues processed: 47 average time/residue: 0.2427 time to fit residues: 14.5351 Evaluate side-chains 43 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 496 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 29 optimal weight: 0.9990 chunk 26 optimal weight: 0.0980 chunk 38 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 14 optimal weight: 0.0970 chunk 44 optimal weight: 0.7980 chunk 18 optimal weight: 0.0870 chunk 41 optimal weight: 0.9980 chunk 13 optimal weight: 0.0870 chunk 1 optimal weight: 0.3980 overall best weight: 0.1534 ------------------------------------------------------------------------------- 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 = 0.3204 r_free = 0.3204 target = 0.105124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.091765 restraints weight = 5646.315| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.76 r_work: 0.2929 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4143 Z= 0.123 Angle : 0.513 5.269 5616 Z= 0.262 Chirality : 0.041 0.156 593 Planarity : 0.004 0.032 741 Dihedral : 5.282 75.515 567 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.88 % Allowed : 12.44 % 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: 0.81 (0.40), residues: 493 helix: 1.71 (0.45), residues: 140 sheet: 0.93 (0.59), residues: 88 loop : -0.20 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 592 HIS 0.003 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 Details of bonding type rmsd hydrogen bonds : bond 0.03298 ( 151) hydrogen bonds : angle 4.87670 ( 426) metal coordination : bond 0.00243 ( 2) covalent geometry : bond 0.00299 ( 4140) covalent geometry : angle 0.51305 ( 5616) Misc. bond : bond 0.00057 ( 1) *********************** 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 46 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.471 Fit side-chains REVERT: A 116 ARG cc_start: 0.8068 (ttp-110) cc_final: 0.7611 (mtm180) REVERT: A 128 PHE cc_start: 0.8848 (p90) cc_final: 0.8479 (p90) REVERT: A 166 GLU cc_start: 0.8110 (tp30) cc_final: 0.7682 (tt0) REVERT: A 169 ASN cc_start: 0.7858 (m-40) cc_final: 0.7637 (m-40) REVERT: A 424 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7386 (tt0) REVERT: A 459 MET cc_start: 0.9204 (mtm) cc_final: 0.8970 (mtm) REVERT: A 595 LYS cc_start: 0.7791 (ttpt) cc_final: 0.7402 (tppt) outliers start: 8 outliers final: 5 residues processed: 45 average time/residue: 0.2223 time to fit residues: 12.2878 Evaluate side-chains 43 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 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 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: 0.8980 chunk 30 optimal weight: 0.8980 chunk 25 optimal weight: 0.0670 chunk 26 optimal weight: 0.0870 chunk 1 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 chunk 41 optimal weight: 0.4980 chunk 21 optimal weight: 0.0270 overall best weight: 0.2354 ------------------------------------------------------------------------------- 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 = 0.3293 r_free = 0.3293 target = 0.108693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.094490 restraints weight = 5621.517| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.85 r_work: 0.2996 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4143 Z= 0.163 Angle : 0.541 5.451 5616 Z= 0.277 Chirality : 0.042 0.168 593 Planarity : 0.004 0.031 741 Dihedral : 5.358 75.999 567 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.82 % Allowed : 11.27 % 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: 0.80 (0.39), residues: 493 helix: 1.71 (0.45), residues: 140 sheet: 0.86 (0.58), 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 0.003 0.001 HIS A 533 PHE 0.009 0.001 PHE A 239 TYR 0.014 0.002 TYR A 102 ARG 0.003 0.000 ARG A 549 Details of bonding type rmsd hydrogen bonds : bond 0.03529 ( 151) hydrogen bonds : angle 4.92066 ( 426) metal coordination : bond 0.00343 ( 2) covalent geometry : bond 0.00400 ( 4140) covalent geometry : angle 0.54091 ( 5616) Misc. bond : bond 0.00087 ( 1) *********************** 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 49 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.519 Fit side-chains REVERT: A 128 PHE cc_start: 0.8861 (p90) cc_final: 0.8518 (p90) REVERT: A 166 GLU cc_start: 0.8192 (tp30) cc_final: 0.7832 (tt0) REVERT: A 169 ASN cc_start: 0.7989 (m-40) cc_final: 0.7779 (m-40) REVERT: A 424 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7527 (tt0) REVERT: A 459 MET cc_start: 0.9184 (mtm) cc_final: 0.8971 (mtm) REVERT: A 595 LYS cc_start: 0.7831 (ttpt) cc_final: 0.7435 (tppt) REVERT: A 601 ARG cc_start: 0.6921 (ptp-170) cc_final: 0.6710 (mtm110) outliers start: 12 outliers final: 7 residues processed: 47 average time/residue: 0.2411 time to fit residues: 13.9209 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 : 0.561 ------------------------------------------------------------------------------- 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: 0.0060 chunk 6 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 0.0970 chunk 32 optimal weight: 0.7980 chunk 48 optimal weight: 0.2980 chunk 47 optimal weight: 0.2980 chunk 35 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 overall best weight: 0.2394 ------------------------------------------------------------------------------- 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 = 0.3308 r_free = 0.3308 target = 0.109643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.095551 restraints weight = 5465.283| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.88 r_work: 0.2985 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4143 Z= 0.165 Angle : 0.549 5.447 5616 Z= 0.283 Chirality : 0.042 0.167 593 Planarity : 0.004 0.030 741 Dihedral : 5.453 77.447 567 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.11 % Allowed : 11.74 % 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: 0.78 (0.39), residues: 493 helix: 1.65 (0.45), residues: 141 sheet: 0.86 (0.58), residues: 88 loop : -0.18 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 592 HIS 0.003 0.001 HIS A 533 PHE 0.008 0.001 PHE A 239 TYR 0.014 0.002 TYR A 102 ARG 0.003 0.000 ARG A 549 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 151) hydrogen bonds : angle 4.93069 ( 426) metal coordination : bond 0.00383 ( 2) covalent geometry : bond 0.00403 ( 4140) covalent geometry : angle 0.54900 ( 5616) Misc. bond : bond 0.00087 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.437 Fit side-chains REVERT: A 116 ARG cc_start: 0.7971 (ttp-110) cc_final: 0.7527 (mtm180) REVERT: A 128 PHE cc_start: 0.8881 (p90) cc_final: 0.8512 (p90) REVERT: A 166 GLU cc_start: 0.8155 (tp30) cc_final: 0.7765 (tt0) REVERT: A 169 ASN cc_start: 0.7963 (m-40) cc_final: 0.7714 (m-40) REVERT: A 424 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7525 (tt0) REVERT: A 459 MET cc_start: 0.9179 (mtm) cc_final: 0.8923 (mtm) REVERT: A 549 ARG cc_start: 0.8361 (mtm-85) cc_final: 0.8019 (mtt-85) outliers start: 9 outliers final: 7 residues processed: 43 average time/residue: 0.2186 time to fit residues: 11.5754 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 : 0.477 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 49 optimal weight: 0.3980 chunk 45 optimal weight: 0.3980 chunk 24 optimal weight: 0.3980 chunk 23 optimal weight: 0.0980 chunk 26 optimal weight: 0.0030 chunk 36 optimal weight: 0.0570 chunk 20 optimal weight: 0.8980 chunk 35 optimal weight: 0.0970 chunk 11 optimal weight: 0.2980 chunk 13 optimal weight: 0.5980 chunk 25 optimal weight: 0.1980 overall best weight: 0.0906 ------------------------------------------------------------------------------- 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 = 0.112419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.098520 restraints weight = 5462.503| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.83 r_work: 0.3034 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4143 Z= 0.102 Angle : 0.506 5.212 5616 Z= 0.259 Chirality : 0.040 0.155 593 Planarity : 0.004 0.031 741 Dihedral : 5.174 75.804 567 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.41 % Allowed : 12.44 % 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: 0.79 (0.39), residues: 493 helix: 1.87 (0.45), residues: 140 sheet: 0.43 (0.55), residues: 98 loop : -0.14 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 592 HIS 0.006 0.001 HIS A 533 PHE 0.010 0.001 PHE A 265 TYR 0.009 0.001 TYR A 157 ARG 0.003 0.000 ARG A 549 Details of bonding type rmsd hydrogen bonds : bond 0.02947 ( 151) hydrogen bonds : angle 4.74468 ( 426) metal coordination : bond 0.00136 ( 2) covalent geometry : bond 0.00241 ( 4140) covalent geometry : angle 0.50611 ( 5616) Misc. bond : bond 0.00040 ( 1) *********************** 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: 6 poor density : 38 time to evaluate : 0.520 Fit side-chains REVERT: A 116 ARG cc_start: 0.7976 (ttp-110) cc_final: 0.7542 (mtm180) REVERT: A 128 PHE cc_start: 0.8822 (p90) cc_final: 0.8452 (p90) REVERT: A 166 GLU cc_start: 0.8121 (tp30) cc_final: 0.7796 (tt0) REVERT: A 424 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7502 (tt0) REVERT: A 459 MET cc_start: 0.9097 (mtm) cc_final: 0.8870 (mtm) REVERT: A 595 LYS cc_start: 0.7787 (ttpt) cc_final: 0.7485 (tppt) outliers start: 6 outliers final: 5 residues processed: 42 average time/residue: 0.2679 time to fit residues: 13.9606 Evaluate side-chains 40 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER 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: 0.0980 chunk 22 optimal weight: 0.0870 chunk 19 optimal weight: 0.0370 chunk 36 optimal weight: 0.1980 chunk 0 optimal weight: 0.9990 chunk 23 optimal weight: 0.1980 chunk 30 optimal weight: 0.0770 chunk 8 optimal weight: 0.1980 chunk 34 optimal weight: 0.0970 chunk 2 optimal weight: 0.0070 chunk 46 optimal weight: 0.0970 overall best weight: 0.0610 ------------------------------------------------------------------------------- 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 = 0.3372 r_free = 0.3372 target = 0.114546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.100467 restraints weight = 5501.015| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.85 r_work: 0.3064 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4143 Z= 0.095 Angle : 0.506 6.536 5616 Z= 0.256 Chirality : 0.040 0.201 593 Planarity : 0.004 0.033 741 Dihedral : 4.796 69.039 567 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.17 % Allowed : 12.21 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.39), residues: 493 helix: 2.04 (0.45), residues: 140 sheet: 0.37 (0.55), residues: 98 loop : -0.10 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 592 HIS 0.005 0.001 HIS A 533 PHE 0.010 0.001 PHE A 265 TYR 0.009 0.001 TYR A 157 ARG 0.003 0.000 ARG A 549 Details of bonding type rmsd hydrogen bonds : bond 0.02775 ( 151) hydrogen bonds : angle 4.56599 ( 426) metal coordination : bond 0.00096 ( 2) covalent geometry : bond 0.00223 ( 4140) covalent geometry : angle 0.50639 ( 5616) Misc. bond : bond 0.00028 ( 1) ********************** 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 49 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.514 Fit side-chains REVERT: A 116 ARG cc_start: 0.7844 (ttp-110) cc_final: 0.7612 (mtm-85) REVERT: A 128 PHE cc_start: 0.8820 (p90) cc_final: 0.8450 (p90) REVERT: A 166 GLU cc_start: 0.8159 (tp30) cc_final: 0.7816 (tt0) REVERT: A 190 TYR cc_start: 0.8818 (t80) cc_final: 0.8565 (t80) REVERT: A 459 MET cc_start: 0.9056 (mtm) cc_final: 0.8733 (mtm) REVERT: A 549 ARG cc_start: 0.8141 (mtm-85) cc_final: 0.7877 (mtt-85) outliers start: 5 outliers final: 5 residues processed: 48 average time/residue: 0.2372 time to fit residues: 14.5810 Evaluate side-chains 41 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 333 LEU 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: 0.3980 chunk 1 optimal weight: 0.6980 chunk 13 optimal weight: 0.4980 chunk 43 optimal weight: 0.2980 chunk 18 optimal weight: 0.3980 chunk 19 optimal weight: 0.0770 chunk 34 optimal weight: 0.0670 chunk 30 optimal weight: 0.5980 chunk 29 optimal weight: 0.3980 chunk 38 optimal weight: 0.7980 chunk 32 optimal weight: 0.2980 overall best weight: 0.2276 ------------------------------------------------------------------------------- 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 = 0.3316 r_free = 0.3316 target = 0.110305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.096094 restraints weight = 5503.201| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.84 r_work: 0.3005 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4143 Z= 0.158 Angle : 0.555 6.640 5616 Z= 0.282 Chirality : 0.043 0.181 593 Planarity : 0.004 0.033 741 Dihedral : 4.943 66.388 567 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.41 % Allowed : 11.97 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.39), residues: 493 helix: 1.94 (0.45), residues: 138 sheet: 0.76 (0.59), residues: 88 loop : -0.16 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 592 HIS 0.004 0.001 HIS A 533 PHE 0.008 0.002 PHE A 239 TYR 0.014 0.002 TYR A 102 ARG 0.003 0.000 ARG A 549 Details of bonding type rmsd hydrogen bonds : bond 0.03463 ( 151) hydrogen bonds : angle 4.85075 ( 426) metal coordination : bond 0.00372 ( 2) covalent geometry : bond 0.00389 ( 4140) covalent geometry : angle 0.55498 ( 5616) Misc. bond : bond 0.00081 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3821.48 seconds wall clock time: 69 minutes 11.71 seconds (4151.71 seconds total)