Starting phenix.real_space_refine on Wed Mar 5 23:43:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v3q_42950/03_2025/8v3q_42950.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v3q_42950/03_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_42950/03_2025/8v3q_42950.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v3q_42950/03_2025/8v3q_42950.map" model { file = "/net/cci-nas-00/data/ceres_data/8v3q_42950/03_2025/8v3q_42950.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v3q_42950/03_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-5624/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: 5.77, per 1000 atoms: 1.43 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: 1.03 Conformation dependent library (CDL) restraints added in 498.6 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: 1.26 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: 7.040 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.470 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:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.020 ------------------------------------------------------------------------------- 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 : 0.508 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: 0.2416 time to fit residues: 18.8781 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 : 0.423 ------------------------------------------------------------------------------- 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: 0.3980 chunk 45 optimal weight: 0.4980 overall best weight: 0.1334 ------------------------------------------------------------------------------- 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 = 0.3237 r_free = 0.3237 target = 0.107719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.094762 restraints weight = 5606.645| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.71 r_work: 0.2976 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4140 Z= 0.193 Angle : 0.556 5.293 5616 Z= 0.291 Chirality : 0.042 0.155 593 Planarity : 0.005 0.041 741 Dihedral : 5.774 79.054 567 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.64 % Allowed : 9.39 % 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: -0.05 (0.37), residues: 493 helix: 0.38 (0.42), residues: 140 sheet: 0.61 (0.56), residues: 92 loop : -0.44 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 592 HIS 0.008 0.001 HIS A 533 PHE 0.011 0.001 PHE A 152 TYR 0.010 0.001 TYR A 102 ARG 0.005 0.001 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: 7 poor density : 53 time to evaluate : 0.478 Fit side-chains REVERT: A 166 GLU cc_start: 0.8049 (tp30) cc_final: 0.7603 (tt0) REVERT: A 169 ASN cc_start: 0.7944 (m-40) cc_final: 0.7570 (m-40) REVERT: A 190 TYR cc_start: 0.8705 (t80) cc_final: 0.8310 (t80) REVERT: A 424 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7310 (tt0) REVERT: A 595 LYS cc_start: 0.7623 (ttpt) cc_final: 0.6732 (mttt) outliers start: 7 outliers final: 3 residues processed: 59 average time/residue: 0.2097 time to fit residues: 15.1018 Evaluate side-chains 37 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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: 0.0570 chunk 42 optimal weight: 0.0980 chunk 40 optimal weight: 0.6980 chunk 47 optimal weight: 0.0970 chunk 34 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 45 optimal weight: 0.0870 chunk 37 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 0.3980 overall best weight: 0.1474 ------------------------------------------------------------------------------- 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 = 0.3236 r_free = 0.3236 target = 0.107498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.094025 restraints weight = 5641.885| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.78 r_work: 0.2961 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2116 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= 0.192 Angle : 0.527 5.204 5616 Z= 0.272 Chirality : 0.041 0.152 593 Planarity : 0.004 0.037 741 Dihedral : 5.395 74.387 567 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.41 % Allowed : 11.03 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.39), residues: 493 helix: 1.08 (0.44), 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 0.007 0.001 TRP A 592 HIS 0.005 0.001 HIS A 533 PHE 0.009 0.001 PHE A 265 TYR 0.012 0.001 TYR A 102 ARG 0.004 0.000 ARG A 549 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.780 Fit side-chains REVERT: A 166 GLU cc_start: 0.8076 (tp30) cc_final: 0.7673 (tt0) REVERT: A 169 ASN cc_start: 0.7911 (m-40) cc_final: 0.7675 (m-40) REVERT: A 424 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7352 (tt0) REVERT: A 459 MET cc_start: 0.9177 (mtm) cc_final: 0.8930 (mtm) REVERT: A 595 LYS cc_start: 0.7731 (ttpt) cc_final: 0.6820 (mttt) outliers start: 6 outliers final: 3 residues processed: 47 average time/residue: 0.2103 time to fit residues: 12.9142 Evaluate side-chains 43 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.1980 chunk 29 optimal weight: 0.3980 chunk 6 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 46 optimal weight: 0.1980 chunk 38 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 chunk 9 optimal weight: 0.1980 overall best weight: 0.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 336 HIS A 533 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.103217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.089879 restraints weight = 5770.427| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.77 r_work: 0.2900 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4140 Z= 0.321 Angle : 0.572 5.358 5616 Z= 0.296 Chirality : 0.043 0.166 593 Planarity : 0.004 0.032 741 Dihedral : 5.569 75.511 567 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.82 % Allowed : 10.56 % 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: 0.71 (0.39), residues: 493 helix: 1.34 (0.46), residues: 140 sheet: 1.38 (0.61), residues: 82 loop : -0.25 (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 0.010 0.002 PHE A 143 TYR 0.017 0.002 TYR A 102 ARG 0.005 0.001 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 50 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.469 Fit side-chains REVERT: A 166 GLU cc_start: 0.8072 (tp30) cc_final: 0.7662 (tt0) REVERT: A 169 ASN cc_start: 0.7941 (m-40) cc_final: 0.7696 (m-40) REVERT: A 424 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7404 (tt0) REVERT: A 496 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8440 (tm-30) REVERT: A 595 LYS cc_start: 0.7835 (ttpt) cc_final: 0.7378 (tppt) outliers start: 12 outliers final: 6 residues processed: 48 average time/residue: 0.2267 time to fit residues: 13.3217 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 : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 569 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.7980 chunk 44 optimal weight: 0.0570 chunk 45 optimal weight: 0.4980 chunk 39 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 13 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 0.1980 chunk 25 optimal weight: 0.0770 chunk 23 optimal weight: 0.1980 chunk 28 optimal weight: 0.1980 overall best weight: 0.1456 ------------------------------------------------------------------------------- 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 = 0.3205 r_free = 0.3205 target = 0.105190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.091791 restraints weight = 5781.901| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.78 r_work: 0.2925 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4140 Z= 0.186 Angle : 0.512 5.188 5616 Z= 0.262 Chirality : 0.041 0.155 593 Planarity : 0.004 0.032 741 Dihedral : 5.380 76.717 567 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % 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: 0.71 (0.39), residues: 493 helix: 1.56 (0.45), residues: 140 sheet: 0.79 (0.56), residues: 92 loop : -0.20 (0.40), residues: 261 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 0.015 0.001 PHE A 128 TYR 0.010 0.001 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 47 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.464 Fit side-chains REVERT: A 116 ARG cc_start: 0.7970 (ttp-110) cc_final: 0.7506 (mtm180) REVERT: A 166 GLU cc_start: 0.8089 (tp30) cc_final: 0.7683 (tt0) REVERT: A 169 ASN cc_start: 0.7880 (m-40) cc_final: 0.7648 (m-40) REVERT: A 424 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7373 (tt0) REVERT: A 459 MET cc_start: 0.9183 (mtm) cc_final: 0.8949 (mtm) REVERT: A 595 LYS cc_start: 0.7752 (ttpt) cc_final: 0.7335 (tppt) REVERT: A 601 ARG cc_start: 0.6803 (ptp-170) cc_final: 0.6454 (ptp-170) outliers start: 9 outliers final: 5 residues processed: 45 average time/residue: 0.2180 time to fit residues: 11.9987 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 : 0.481 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 29 optimal weight: 0.9990 chunk 26 optimal weight: 0.3980 chunk 38 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 chunk 14 optimal weight: 0.0870 chunk 44 optimal weight: 0.1980 chunk 18 optimal weight: 0.0980 chunk 41 optimal weight: 0.7980 chunk 13 optimal weight: 0.0870 chunk 1 optimal weight: 0.6980 overall best weight: 0.1736 ------------------------------------------------------------------------------- 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 = 0.3332 r_free = 0.3332 target = 0.111411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.096750 restraints weight = 5564.395| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.95 r_work: 0.2999 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4140 Z= 0.210 Angle : 0.522 5.325 5616 Z= 0.266 Chirality : 0.041 0.160 593 Planarity : 0.004 0.032 741 Dihedral : 5.298 75.444 567 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.11 % Allowed : 12.44 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.40), residues: 493 helix: 1.71 (0.45), residues: 140 sheet: 0.92 (0.58), residues: 88 loop : -0.15 (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 0.015 0.001 PHE A 128 TYR 0.011 0.001 TYR A 102 ARG 0.004 0.000 ARG A 549 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.489 Fit side-chains REVERT: A 116 ARG cc_start: 0.7941 (ttp-110) cc_final: 0.7488 (mtm180) REVERT: A 166 GLU cc_start: 0.8173 (tp30) cc_final: 0.7759 (tt0) REVERT: A 169 ASN cc_start: 0.7958 (m-40) cc_final: 0.7695 (m-40) REVERT: A 424 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7442 (tt0) REVERT: A 459 MET cc_start: 0.9191 (mtm) cc_final: 0.8948 (mtm) REVERT: A 549 ARG cc_start: 0.8387 (mtm-85) cc_final: 0.8058 (mtt-85) REVERT: A 595 LYS cc_start: 0.7740 (ttpt) cc_final: 0.7312 (tppt) outliers start: 9 outliers final: 6 residues processed: 46 average time/residue: 0.2239 time to fit residues: 12.6640 Evaluate side-chains 44 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- 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: 0.0770 chunk 26 optimal weight: 0.0970 chunk 1 optimal weight: 0.6980 chunk 11 optimal weight: 0.4980 chunk 45 optimal weight: 0.3980 chunk 46 optimal weight: 0.0770 chunk 33 optimal weight: 0.6980 chunk 41 optimal weight: 0.3980 chunk 21 optimal weight: 0.0030 overall best weight: 0.1304 ------------------------------------------------------------------------------- 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 = 0.112074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.097758 restraints weight = 5589.244| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.89 r_work: 0.3004 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4140 Z= 0.179 Angle : 0.515 5.866 5616 Z= 0.262 Chirality : 0.041 0.156 593 Planarity : 0.004 0.031 741 Dihedral : 5.148 73.320 567 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.35 % Allowed : 11.74 % 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: 0.82 (0.40), residues: 493 helix: 1.85 (0.45), residues: 140 sheet: 0.51 (0.54), residues: 98 loop : -0.11 (0.42), residues: 255 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 0.014 0.001 PHE A 128 TYR 0.009 0.001 TYR A 157 ARG 0.004 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 47 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.535 Fit side-chains REVERT: A 116 ARG cc_start: 0.7962 (ttp-110) cc_final: 0.7518 (mtm180) REVERT: A 166 GLU cc_start: 0.8165 (tp30) cc_final: 0.7805 (tt0) REVERT: A 169 ASN cc_start: 0.7968 (m-40) cc_final: 0.7767 (m-40) REVERT: A 424 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7413 (tt0) REVERT: A 459 MET cc_start: 0.9168 (mtm) cc_final: 0.8951 (mtm) REVERT: A 549 ARG cc_start: 0.8336 (mtm-85) cc_final: 0.8007 (mtt-85) REVERT: A 595 LYS cc_start: 0.7804 (ttpt) cc_final: 0.7441 (tppt) outliers start: 10 outliers final: 7 residues processed: 45 average time/residue: 0.2601 time to fit residues: 14.1757 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 : 0.477 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 16 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 3 optimal weight: 0.0970 chunk 32 optimal weight: 0.6980 chunk 48 optimal weight: 0.3980 chunk 47 optimal weight: 0.0670 chunk 35 optimal weight: 0.6980 chunk 21 optimal weight: 0.4980 overall best weight: 0.3116 ------------------------------------------------------------------------------- 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 = 0.3279 r_free = 0.3279 target = 0.107779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.093512 restraints weight = 5516.667| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.84 r_work: 0.2975 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4140 Z= 0.325 Angle : 0.575 6.637 5616 Z= 0.293 Chirality : 0.044 0.175 593 Planarity : 0.004 0.034 741 Dihedral : 5.376 73.440 567 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.35 % Allowed : 11.74 % 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: 0.76 (0.39), residues: 493 helix: 1.62 (0.45), residues: 139 sheet: 0.89 (0.57), residues: 90 loop : -0.19 (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 0.016 0.002 PHE A 128 TYR 0.017 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 44 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.660 Fit side-chains REVERT: A 116 ARG cc_start: 0.7989 (ttp-110) cc_final: 0.7531 (mtm180) REVERT: A 128 PHE cc_start: 0.8815 (p90) cc_final: 0.8459 (p90) REVERT: A 166 GLU cc_start: 0.8157 (tp30) cc_final: 0.7810 (tt0) REVERT: A 169 ASN cc_start: 0.8004 (m-40) cc_final: 0.7666 (m-40) REVERT: A 424 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7498 (tt0) REVERT: A 459 MET cc_start: 0.9151 (mtm) cc_final: 0.8928 (mtm) REVERT: A 549 ARG cc_start: 0.8476 (mtm-85) cc_final: 0.8136 (mtt-85) outliers start: 10 outliers final: 8 residues processed: 42 average time/residue: 0.2815 time to fit residues: 15.5487 Evaluate side-chains 42 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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: 0.0980 chunk 45 optimal weight: 0.1980 chunk 24 optimal weight: 0.0970 chunk 23 optimal weight: 0.0970 chunk 26 optimal weight: 0.0980 chunk 36 optimal weight: 0.0970 chunk 20 optimal weight: 0.7980 chunk 35 optimal weight: 0.0870 chunk 11 optimal weight: 0.6980 chunk 13 optimal weight: 0.3980 chunk 25 optimal weight: 0.0770 overall best weight: 0.0910 ------------------------------------------------------------------------------- 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 = 0.3335 r_free = 0.3335 target = 0.111689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.097600 restraints weight = 5493.762| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.90 r_work: 0.3016 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2895 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= 0.152 Angle : 0.495 5.259 5616 Z= 0.253 Chirality : 0.040 0.156 593 Planarity : 0.004 0.033 741 Dihedral : 5.110 73.656 567 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.64 % Allowed : 12.68 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.40), residues: 493 helix: 1.86 (0.45), residues: 140 sheet: 0.87 (0.58), residues: 88 loop : -0.16 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 592 HIS 0.004 0.001 HIS A 533 PHE 0.012 0.001 PHE A 128 TYR 0.008 0.001 TYR A 157 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 42 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.476 Fit side-chains REVERT: A 116 ARG cc_start: 0.7873 (ttp-110) cc_final: 0.7428 (mtm180) REVERT: A 128 PHE cc_start: 0.8795 (p90) cc_final: 0.8449 (p90) REVERT: A 166 GLU cc_start: 0.8108 (tp30) cc_final: 0.7744 (tt0) REVERT: A 169 ASN cc_start: 0.7958 (m-40) cc_final: 0.7705 (m-40) REVERT: A 424 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7520 (tt0) REVERT: A 459 MET cc_start: 0.9194 (mtm) cc_final: 0.8967 (mtm) REVERT: A 549 ARG cc_start: 0.8355 (mtm-85) cc_final: 0.7994 (mtt-85) REVERT: A 595 LYS cc_start: 0.7741 (ttpt) cc_final: 0.7320 (tppt) outliers start: 7 outliers final: 5 residues processed: 41 average time/residue: 0.2418 time to fit residues: 12.9066 Evaluate side-chains 39 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 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 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: 0.3980 chunk 22 optimal weight: 0.0870 chunk 19 optimal weight: 0.0170 chunk 36 optimal weight: 0.0570 chunk 0 optimal weight: 0.9990 chunk 23 optimal weight: 0.0980 chunk 30 optimal weight: 0.6980 chunk 8 optimal weight: 0.0980 chunk 34 optimal weight: 0.0870 chunk 2 optimal weight: 0.0000 chunk 46 optimal weight: 0.0980 overall best weight: 0.0496 ------------------------------------------------------------------------------- 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 = 0.3369 r_free = 0.3369 target = 0.114425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.099904 restraints weight = 5507.122| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.96 r_work: 0.3053 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4140 Z= 0.133 Angle : 0.485 5.128 5616 Z= 0.246 Chirality : 0.039 0.153 593 Planarity : 0.004 0.035 741 Dihedral : 4.722 67.002 567 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.17 % Allowed : 13.15 % 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: 0.92 (0.40), residues: 493 helix: 2.08 (0.45), residues: 140 sheet: 0.53 (0.57), residues: 91 loop : -0.13 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 592 HIS 0.006 0.001 HIS A 533 PHE 0.012 0.001 PHE A 128 TYR 0.008 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 42 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.480 Fit side-chains REVERT: A 166 GLU cc_start: 0.8117 (tp30) cc_final: 0.7745 (tt0) REVERT: A 169 ASN cc_start: 0.7973 (m-40) cc_final: 0.7729 (m-40) REVERT: A 190 TYR cc_start: 0.8936 (t80) cc_final: 0.8633 (t80) REVERT: A 424 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7479 (tt0) REVERT: A 459 MET cc_start: 0.9133 (mtm) cc_final: 0.8842 (mtm) REVERT: A 549 ARG cc_start: 0.8287 (mtm-85) cc_final: 0.7949 (mtt-85) REVERT: A 595 LYS cc_start: 0.7630 (ttpt) cc_final: 0.7365 (tppt) outliers start: 5 outliers final: 5 residues processed: 41 average time/residue: 0.1949 time to fit residues: 10.3085 Evaluate side-chains 37 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 528 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 44 optimal weight: 0.0370 chunk 1 optimal weight: 0.5980 chunk 13 optimal weight: 0.0670 chunk 43 optimal weight: 0.3980 chunk 18 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 0.0770 chunk 30 optimal weight: 0.6980 chunk 29 optimal weight: 0.0030 chunk 38 optimal weight: 0.5980 chunk 32 optimal weight: 0.0050 overall best weight: 0.0378 ------------------------------------------------------------------------------- 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 = 0.3362 r_free = 0.3362 target = 0.113870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.099402 restraints weight = 5456.777| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.93 r_work: 0.3051 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3091 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= 0.130 Angle : 0.488 6.849 5616 Z= 0.246 Chirality : 0.039 0.182 593 Planarity : 0.004 0.035 741 Dihedral : 4.514 62.262 567 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.17 % Allowed : 13.62 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.40), residues: 493 helix: 2.15 (0.45), residues: 140 sheet: 0.36 (0.54), residues: 98 loop : -0.03 (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 0.012 0.001 PHE A 128 TYR 0.009 0.001 TYR A 157 ARG 0.003 0.000 ARG A 549 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2987.57 seconds wall clock time: 53 minutes 51.72 seconds (3231.72 seconds total)