Starting phenix.real_space_refine on Sat Dec 28 02:11:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b0m_15788/12_2024/8b0m_15788.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b0m_15788/12_2024/8b0m_15788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8b0m_15788/12_2024/8b0m_15788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b0m_15788/12_2024/8b0m_15788.map" model { file = "/net/cci-nas-00/data/ceres_data/8b0m_15788/12_2024/8b0m_15788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b0m_15788/12_2024/8b0m_15788.cif" } resolution = 3.01 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= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3853 atoms to isotropic. 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 P 1 5.49 5 S 14 5.16 5 C 2648 2.51 5 N 656 2.21 5 O 696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4015 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3965 Classifications: {'peptide': 508} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 36, 'TRANS': 471} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.11, per 1000 atoms: 0.77 Number of scatterers: 4015 At special positions: 0 Unit cell: (59.472, 83.426, 84.252, 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) S 14 16.00 P 1 15.00 O 696 8.00 N 656 7.00 C 2648 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=0, symmetry=0 Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 482.1 milliseconds 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 936 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 4 sheets defined 59.4% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 Processing helix chain 'A' and resid 9 through 23 Processing helix chain 'A' and resid 24 through 28 removed outlier: 3.599A pdb=" N PHE A 28 " --> pdb=" O THR A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 47 removed outlier: 3.919A pdb=" N ILE A 38 " --> pdb=" O TRP A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 69 removed outlier: 3.509A pdb=" N ALA A 57 " --> pdb=" O PRO A 53 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 81 removed outlier: 3.527A pdb=" N SER A 78 " --> pdb=" O TRP A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 116 removed outlier: 4.200A pdb=" N TYR A 104 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 127 through 140 Processing helix chain 'A' and resid 141 through 145 removed outlier: 3.839A pdb=" N THR A 144 " --> pdb=" O TRP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 155 removed outlier: 4.022A pdb=" N SER A 154 " --> pdb=" O GLN A 150 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 150 through 155' Processing helix chain 'A' and resid 156 through 157 No H-bonds generated for 'chain 'A' and resid 156 through 157' Processing helix chain 'A' and resid 158 through 162 removed outlier: 4.607A pdb=" N GLY A 162 " --> pdb=" O PRO A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 168 Processing helix chain 'A' and resid 168 through 189 removed outlier: 3.894A pdb=" N ILE A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 204 removed outlier: 3.965A pdb=" N PHE A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 211 Processing helix chain 'A' and resid 238 through 240 No H-bonds generated for 'chain 'A' and resid 238 through 240' Processing helix chain 'A' and resid 241 through 257 Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 277 through 292 removed outlier: 3.611A pdb=" N LEU A 281 " --> pdb=" O GLN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 349 removed outlier: 4.441A pdb=" N SER A 349 " --> pdb=" O PRO A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.694A pdb=" N LEU A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 350 through 355' Processing helix chain 'A' and resid 356 through 359 Processing helix chain 'A' and resid 386 through 391 Processing helix chain 'A' and resid 392 through 400 Processing helix chain 'A' and resid 412 through 417 removed outlier: 4.385A pdb=" N TRP A 415 " --> pdb=" O ASN A 412 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY A 417 " --> pdb=" O ALA A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 437 removed outlier: 3.570A pdb=" N ARG A 432 " --> pdb=" O MET A 428 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA A 433 " --> pdb=" O ALA A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 487 Processing helix chain 'A' and resid 488 through 508 removed outlier: 4.087A pdb=" N MET A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 215 through 216 Processing sheet with id=AA2, first strand: chain 'A' and resid 270 through 273 removed outlier: 3.940A pdb=" N VAL A 300 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ASP A 272 " --> pdb=" O VAL A 300 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 270 through 273 removed outlier: 3.940A pdb=" N VAL A 300 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ASP A 272 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE A 263 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N GLY A 298 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU A 262 " --> pdb=" O GLN A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 375 through 377 removed outlier: 6.534A pdb=" N GLU A 381 " --> pdb=" O TYR A 406 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LEU A 408 " --> pdb=" O GLU A 381 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N THR A 383 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ILE A 410 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU A 407 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N SER A 443 " --> pdb=" O LEU A 407 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR A 409 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL A 451 " --> pdb=" O GLN A 459 " (cutoff:3.500A) 204 hydrogen bonds defined for protein. 543 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: 1.18 Time building geometry restraints manager: 1.18 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: 613 1.31 - 1.43: 1113 1.43 - 1.56: 2374 1.56 - 1.68: 2 1.68 - 1.80: 26 Bond restraints: 4128 Sorted by residual: bond pdb=" C8 PTY A 601 " pdb=" O7 PTY A 601 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" C30 PTY A 601 " pdb=" O4 PTY A 601 " ideal model delta sigma weight residual 1.331 1.398 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C6 PTY A 601 " pdb=" O7 PTY A 601 " ideal model delta sigma weight residual 1.432 1.396 0.036 2.00e-02 2.50e+03 3.18e+00 bond pdb=" C1 PTY A 601 " pdb=" O4 PTY A 601 " ideal model delta sigma weight residual 1.427 1.396 0.031 2.00e-02 2.50e+03 2.36e+00 bond pdb=" C3 PTY A 601 " pdb=" O11 PTY A 601 " ideal model delta sigma weight residual 1.420 1.398 0.022 2.00e-02 2.50e+03 1.23e+00 ... (remaining 4123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 5579 3.27 - 6.55: 49 6.55 - 9.82: 2 9.82 - 13.09: 1 13.09 - 16.37: 1 Bond angle restraints: 5632 Sorted by residual: angle pdb=" O11 PTY A 601 " pdb=" P1 PTY A 601 " pdb=" O14 PTY A 601 " ideal model delta sigma weight residual 92.90 109.27 -16.37 3.00e+00 1.11e-01 2.98e+01 angle pdb=" O12 PTY A 601 " pdb=" P1 PTY A 601 " pdb=" O13 PTY A 601 " ideal model delta sigma weight residual 119.61 109.68 9.93 3.00e+00 1.11e-01 1.10e+01 angle pdb=" C11 PTY A 601 " pdb=" C8 PTY A 601 " pdb=" O7 PTY A 601 " ideal model delta sigma weight residual 111.29 119.69 -8.40 3.00e+00 1.11e-01 7.83e+00 angle pdb=" C31 PTY A 601 " pdb=" C30 PTY A 601 " pdb=" O4 PTY A 601 " ideal model delta sigma weight residual 111.62 119.81 -8.19 3.00e+00 1.11e-01 7.46e+00 angle pdb=" N GLU A 219 " pdb=" CA GLU A 219 " pdb=" C GLU A 219 " ideal model delta sigma weight residual 113.18 109.62 3.56 1.33e+00 5.65e-01 7.15e+00 ... (remaining 5627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.60: 2347 22.60 - 45.21: 66 45.21 - 67.81: 11 67.81 - 90.41: 1 90.41 - 113.02: 1 Dihedral angle restraints: 2426 sinusoidal: 966 harmonic: 1460 Sorted by residual: dihedral pdb=" CA GLY A 71 " pdb=" C GLY A 71 " pdb=" N ILE A 72 " pdb=" CA ILE A 72 " ideal model delta harmonic sigma weight residual 180.00 155.62 24.38 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" C3 PTY A 601 " pdb=" O11 PTY A 601 " pdb=" P1 PTY A 601 " pdb=" O12 PTY A 601 " ideal model delta sinusoidal sigma weight residual -59.77 53.25 -113.02 1 3.00e+01 1.11e-03 1.48e+01 dihedral pdb=" CA PHE A 28 " pdb=" C PHE A 28 " pdb=" N SER A 29 " pdb=" CA SER A 29 " ideal model delta harmonic sigma weight residual -180.00 -161.99 -18.01 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 2423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 374 0.029 - 0.057: 165 0.057 - 0.086: 49 0.086 - 0.114: 38 0.114 - 0.143: 8 Chirality restraints: 634 Sorted by residual: chirality pdb=" CA TRP A 489 " pdb=" N TRP A 489 " pdb=" C TRP A 489 " pdb=" CB TRP A 489 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA ILE A 316 " pdb=" N ILE A 316 " pdb=" C ILE A 316 " pdb=" CB ILE A 316 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA ILE A 72 " pdb=" N ILE A 72 " pdb=" C ILE A 72 " pdb=" CB ILE A 72 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 631 not shown) Planarity restraints: 705 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 421 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO A 422 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 422 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 422 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 87 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO A 88 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 88 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 88 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 204 " -0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO A 205 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 205 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 205 " -0.019 5.00e-02 4.00e+02 ... (remaining 702 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 939 2.79 - 3.31: 3875 3.31 - 3.84: 6778 3.84 - 4.37: 8433 4.37 - 4.90: 14419 Nonbonded interactions: 34444 Sorted by model distance: nonbonded pdb=" O VAL A 77 " pdb=" OG1 THR A 81 " model vdw 2.258 3.040 nonbonded pdb=" OH TYR A 333 " pdb=" OE1 GLU A 389 " model vdw 2.269 3.040 nonbonded pdb=" OE1 GLU A 274 " pdb=" NH2 ARG A 332 " model vdw 2.303 3.120 nonbonded pdb=" O ALA A 98 " pdb=" OG SER A 102 " model vdw 2.327 3.040 nonbonded pdb=" OE1 GLU A 136 " pdb=" NH2 ARG A 139 " model vdw 2.344 3.120 ... (remaining 34439 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 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: 14.010 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 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 : 0.003 0.068 4128 Z= 0.209 Angle : 0.656 16.367 5632 Z= 0.283 Chirality : 0.042 0.143 634 Planarity : 0.005 0.041 705 Dihedral : 11.178 113.017 1490 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.48 % Allowed : 2.40 % Favored : 97.12 % 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: -0.18 (0.39), residues: 506 helix: 0.33 (0.34), residues: 229 sheet: 0.42 (0.73), residues: 65 loop : -0.68 (0.47), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 34 HIS 0.001 0.001 HIS A 425 PHE 0.009 0.001 PHE A 28 TYR 0.008 0.001 TYR A 31 ARG 0.001 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.391 Fit side-chains REVERT: A 11 ARG cc_start: 0.7011 (mtt90) cc_final: 0.6811 (mtm180) REVERT: A 238 ASP cc_start: 0.8267 (m-30) cc_final: 0.7863 (m-30) REVERT: A 247 LYS cc_start: 0.8697 (ttpp) cc_final: 0.8431 (ttmm) REVERT: A 278 GLN cc_start: 0.9247 (tp-100) cc_final: 0.9037 (tp40) REVERT: A 282 LYS cc_start: 0.8595 (mttt) cc_final: 0.8270 (mttp) outliers start: 2 outliers final: 2 residues processed: 73 average time/residue: 0.2041 time to fit residues: 18.0407 Evaluate side-chains 44 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 500 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.9980 chunk 37 optimal weight: 0.0050 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 20 optimal weight: 0.0980 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4128 Z= 0.179 Angle : 0.556 5.721 5632 Z= 0.283 Chirality : 0.044 0.166 634 Planarity : 0.005 0.042 705 Dihedral : 9.599 78.818 594 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.72 % Allowed : 6.97 % Favored : 92.31 % 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: 0.13 (0.39), residues: 506 helix: 0.80 (0.34), residues: 231 sheet: 0.26 (0.75), residues: 60 loop : -0.68 (0.47), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 34 HIS 0.001 0.001 HIS A 425 PHE 0.015 0.001 PHE A 500 TYR 0.007 0.001 TYR A 313 ARG 0.002 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.481 Fit side-chains REVERT: A 11 ARG cc_start: 0.6895 (mtt90) cc_final: 0.6319 (mtm180) REVERT: A 19 LEU cc_start: 0.6840 (mt) cc_final: 0.6536 (tp) REVERT: A 238 ASP cc_start: 0.8442 (m-30) cc_final: 0.8015 (m-30) REVERT: A 247 LYS cc_start: 0.8662 (ttpp) cc_final: 0.8370 (ttmm) outliers start: 3 outliers final: 3 residues processed: 48 average time/residue: 0.1849 time to fit residues: 11.3075 Evaluate side-chains 40 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 500 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 7.9990 chunk 14 optimal weight: 0.0370 chunk 37 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 12 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.5460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4128 Z= 0.173 Angle : 0.528 5.768 5632 Z= 0.265 Chirality : 0.043 0.160 634 Planarity : 0.005 0.042 705 Dihedral : 9.080 63.079 594 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.68 % Allowed : 6.73 % Favored : 91.59 % 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: 0.22 (0.39), residues: 506 helix: 1.06 (0.34), residues: 232 sheet: 0.23 (0.72), residues: 62 loop : -0.87 (0.46), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 34 HIS 0.001 0.001 HIS A 425 PHE 0.012 0.001 PHE A 174 TYR 0.007 0.001 TYR A 104 ARG 0.001 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.456 Fit side-chains REVERT: A 19 LEU cc_start: 0.6765 (mt) cc_final: 0.6519 (tp) REVERT: A 238 ASP cc_start: 0.8475 (m-30) cc_final: 0.8031 (m-30) REVERT: A 247 LYS cc_start: 0.8663 (ttpp) cc_final: 0.8366 (ttmm) outliers start: 7 outliers final: 7 residues processed: 51 average time/residue: 0.1412 time to fit residues: 9.7013 Evaluate side-chains 52 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 500 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4128 Z= 0.241 Angle : 0.549 5.867 5632 Z= 0.276 Chirality : 0.045 0.167 634 Planarity : 0.005 0.044 705 Dihedral : 8.791 66.050 594 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.40 % Allowed : 6.97 % Favored : 90.62 % 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: 0.18 (0.39), residues: 506 helix: 1.12 (0.34), residues: 232 sheet: -0.28 (0.64), residues: 76 loop : -0.86 (0.48), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 34 HIS 0.001 0.000 HIS A 425 PHE 0.014 0.001 PHE A 174 TYR 0.010 0.001 TYR A 104 ARG 0.002 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.469 Fit side-chains REVERT: A 238 ASP cc_start: 0.8485 (m-30) cc_final: 0.8048 (m-30) REVERT: A 247 LYS cc_start: 0.8684 (ttpp) cc_final: 0.8374 (ttmm) outliers start: 10 outliers final: 8 residues processed: 49 average time/residue: 0.1345 time to fit residues: 8.9797 Evaluate side-chains 49 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 500 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 12 optimal weight: 0.0010 chunk 16 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4128 Z= 0.212 Angle : 0.539 5.783 5632 Z= 0.270 Chirality : 0.044 0.161 634 Planarity : 0.005 0.044 705 Dihedral : 8.496 72.968 594 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.64 % Allowed : 7.21 % 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: 0.24 (0.39), residues: 506 helix: 1.24 (0.34), residues: 233 sheet: -0.33 (0.64), residues: 76 loop : -0.89 (0.48), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 34 HIS 0.001 0.000 HIS A 337 PHE 0.012 0.001 PHE A 174 TYR 0.010 0.001 TYR A 104 ARG 0.001 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.462 Fit side-chains REVERT: A 19 LEU cc_start: 0.6952 (OUTLIER) cc_final: 0.6400 (tp) REVERT: A 238 ASP cc_start: 0.8473 (m-30) cc_final: 0.8049 (m-30) REVERT: A 239 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8253 (mm-30) REVERT: A 247 LYS cc_start: 0.8669 (ttpp) cc_final: 0.8352 (ttmm) outliers start: 11 outliers final: 10 residues processed: 47 average time/residue: 0.1281 time to fit residues: 8.3119 Evaluate side-chains 50 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 500 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 40 optimal weight: 0.0470 chunk 22 optimal weight: 4.9990 chunk 4 optimal weight: 0.3980 chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4128 Z= 0.165 Angle : 0.518 5.730 5632 Z= 0.259 Chirality : 0.043 0.158 634 Planarity : 0.005 0.044 705 Dihedral : 8.264 80.355 594 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.88 % Allowed : 7.93 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.40), residues: 506 helix: 1.49 (0.35), residues: 233 sheet: -0.29 (0.64), residues: 76 loop : -0.88 (0.48), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 34 HIS 0.001 0.000 HIS A 425 PHE 0.011 0.001 PHE A 500 TYR 0.008 0.001 TYR A 104 ARG 0.001 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.414 Fit side-chains REVERT: A 19 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6329 (tp) REVERT: A 238 ASP cc_start: 0.8499 (m-30) cc_final: 0.8052 (m-30) REVERT: A 247 LYS cc_start: 0.8666 (ttpp) cc_final: 0.8347 (ttmm) outliers start: 12 outliers final: 11 residues processed: 50 average time/residue: 0.1225 time to fit residues: 8.5288 Evaluate side-chains 56 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 500 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4128 Z= 0.221 Angle : 0.540 5.781 5632 Z= 0.270 Chirality : 0.044 0.160 634 Planarity : 0.005 0.045 705 Dihedral : 8.217 83.165 594 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.88 % Allowed : 8.17 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.40), residues: 506 helix: 1.50 (0.35), residues: 233 sheet: -0.25 (0.64), residues: 76 loop : -0.92 (0.48), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 34 HIS 0.001 0.000 HIS A 337 PHE 0.012 0.001 PHE A 174 TYR 0.010 0.001 TYR A 104 ARG 0.001 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.495 Fit side-chains REVERT: A 19 LEU cc_start: 0.6877 (OUTLIER) cc_final: 0.6377 (tp) REVERT: A 238 ASP cc_start: 0.8512 (m-30) cc_final: 0.8074 (m-30) REVERT: A 247 LYS cc_start: 0.8653 (ttpp) cc_final: 0.8326 (ttmm) outliers start: 12 outliers final: 11 residues processed: 51 average time/residue: 0.1281 time to fit residues: 8.9703 Evaluate side-chains 57 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 500 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4128 Z= 0.192 Angle : 0.533 5.764 5632 Z= 0.267 Chirality : 0.044 0.158 634 Planarity : 0.005 0.045 705 Dihedral : 8.162 87.994 594 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.88 % Allowed : 8.17 % Favored : 88.94 % 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: 0.51 (0.40), residues: 506 helix: 1.58 (0.35), residues: 233 sheet: -0.16 (0.64), residues: 76 loop : -0.93 (0.48), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 34 HIS 0.001 0.000 HIS A 337 PHE 0.012 0.001 PHE A 500 TYR 0.009 0.001 TYR A 104 ARG 0.001 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.475 Fit side-chains REVERT: A 19 LEU cc_start: 0.6863 (OUTLIER) cc_final: 0.6351 (tp) REVERT: A 238 ASP cc_start: 0.8481 (m-30) cc_final: 0.8082 (m-30) REVERT: A 247 LYS cc_start: 0.8653 (ttpp) cc_final: 0.8325 (ttmm) outliers start: 12 outliers final: 11 residues processed: 51 average time/residue: 0.1369 time to fit residues: 9.6358 Evaluate side-chains 58 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 500 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 0.0470 chunk 29 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4128 Z= 0.170 Angle : 0.526 5.855 5632 Z= 0.263 Chirality : 0.043 0.161 634 Planarity : 0.005 0.045 705 Dihedral : 7.956 86.533 594 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.64 % Allowed : 8.17 % Favored : 89.18 % 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: 0.62 (0.40), residues: 506 helix: 1.68 (0.35), residues: 233 sheet: -0.07 (0.64), residues: 76 loop : -0.92 (0.48), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 34 HIS 0.001 0.000 HIS A 337 PHE 0.011 0.001 PHE A 500 TYR 0.009 0.001 TYR A 104 ARG 0.001 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.466 Fit side-chains REVERT: A 19 LEU cc_start: 0.6828 (OUTLIER) cc_final: 0.6343 (tp) REVERT: A 85 MET cc_start: 0.8151 (mtm) cc_final: 0.7765 (ptp) REVERT: A 235 LEU cc_start: 0.8850 (tp) cc_final: 0.8600 (tp) REVERT: A 238 ASP cc_start: 0.8526 (m-30) cc_final: 0.8117 (m-30) REVERT: A 247 LYS cc_start: 0.8650 (ttpp) cc_final: 0.8321 (ttmm) outliers start: 11 outliers final: 10 residues processed: 53 average time/residue: 0.1308 time to fit residues: 9.4715 Evaluate side-chains 57 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 500 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4128 Z= 0.192 Angle : 0.534 5.753 5632 Z= 0.266 Chirality : 0.044 0.158 634 Planarity : 0.005 0.045 705 Dihedral : 7.799 82.491 594 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.64 % Allowed : 8.17 % Favored : 89.18 % 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: 0.63 (0.40), residues: 506 helix: 1.69 (0.35), residues: 233 sheet: -0.07 (0.65), residues: 76 loop : -0.92 (0.48), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 34 HIS 0.001 0.000 HIS A 337 PHE 0.012 0.001 PHE A 500 TYR 0.009 0.001 TYR A 104 ARG 0.001 0.000 ARG A 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.418 Fit side-chains REVERT: A 19 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.6357 (tp) REVERT: A 85 MET cc_start: 0.8198 (mtm) cc_final: 0.7606 (ptp) REVERT: A 235 LEU cc_start: 0.8826 (tp) cc_final: 0.8402 (tp) REVERT: A 238 ASP cc_start: 0.8514 (m-30) cc_final: 0.8112 (m-30) REVERT: A 247 LYS cc_start: 0.8696 (ttpp) cc_final: 0.8362 (ttmm) outliers start: 11 outliers final: 10 residues processed: 53 average time/residue: 0.1237 time to fit residues: 9.0340 Evaluate side-chains 58 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 500 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 0.0980 chunk 34 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3450 r_free = 0.3450 target = 0.125829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.094423 restraints weight = 4969.853| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.36 r_work: 0.2933 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 4128 Z= 0.175 Angle : 0.534 5.784 5632 Z= 0.267 Chirality : 0.044 0.160 634 Planarity : 0.005 0.045 705 Dihedral : 7.683 79.576 594 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.64 % Allowed : 8.17 % Favored : 89.18 % 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: 0.67 (0.40), residues: 506 helix: 1.74 (0.35), residues: 233 sheet: -0.02 (0.65), residues: 76 loop : -0.93 (0.48), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 34 HIS 0.001 0.000 HIS A 337 PHE 0.012 0.001 PHE A 500 TYR 0.009 0.001 TYR A 104 ARG 0.001 0.000 ARG A 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1267.50 seconds wall clock time: 23 minutes 42.51 seconds (1422.51 seconds total)