Starting phenix.real_space_refine on Sun Mar 10 18:05:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuz_26807/03_2024/7uuz_26807_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuz_26807/03_2024/7uuz_26807.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuz_26807/03_2024/7uuz_26807_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuz_26807/03_2024/7uuz_26807_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuz_26807/03_2024/7uuz_26807_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuz_26807/03_2024/7uuz_26807.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuz_26807/03_2024/7uuz_26807.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuz_26807/03_2024/7uuz_26807_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuz_26807/03_2024/7uuz_26807_updated.pdb" } resolution = 3.2 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= -0.004 sd= 0.095 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: 7 Type Number sf(0) Gaussians Re 1 12.26 5 P 1 5.49 5 S 26 5.16 5 Na 1 4.78 5 C 2500 2.51 5 N 591 2.21 5 O 666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 122": "OE1" <-> "OE2" Residue "A GLU 470": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3786 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3786 Unusual residues: {' NA': 1, '3PH': 1, 'REO': 1} Classifications: {'peptide': 501, 'undetermined': 3} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 476, None: 3} Not linked: pdbres="TRP A 560 " pdbres=" NA A 701 " Not linked: pdbres=" NA A 701 " pdbres="REO A 702 " Not linked: pdbres="REO A 702 " pdbres="3PH A 703 " Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 2.67, per 1000 atoms: 0.71 Number of scatterers: 3786 At special positions: 0 Unit cell: (69.42, 77.964, 83.304, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Re 1 74.95 S 26 16.00 P 1 15.00 Na 1 11.00 O 666 8.00 N 591 7.00 C 2500 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 - 3.50 Amino acid : False - 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: 1.84 Conformation dependent library (CDL) restraints added in 722.6 milliseconds 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: 894 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 0 sheets defined 76.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 15 through 36 Processing helix chain 'A' and resid 56 through 67 removed outlier: 4.477A pdb=" N PHE A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 83 Proline residue: A 77 - end of helix Processing helix chain 'A' and resid 87 through 104 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 127 through 159 Proline residue: A 152 - end of helix Processing helix chain 'A' and resid 164 through 180 Processing helix chain 'A' and resid 190 through 213 removed outlier: 3.546A pdb=" N VAL A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 225 Processing helix chain 'A' and resid 244 through 259 removed outlier: 3.685A pdb=" N VAL A 249 " --> pdb=" O TRP A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 272 removed outlier: 3.682A pdb=" N CYS A 272 " --> pdb=" O ARG A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 307 Processing helix chain 'A' and resid 312 through 315 No H-bonds generated for 'chain 'A' and resid 312 through 315' Processing helix chain 'A' and resid 321 through 332 removed outlier: 4.138A pdb=" N MET A 325 " --> pdb=" O ASP A 322 " (cutoff:3.500A) Proline residue: A 326 - end of helix removed outlier: 3.640A pdb=" N VAL A 329 " --> pdb=" O PRO A 326 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 332 " --> pdb=" O VAL A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 369 removed outlier: 3.702A pdb=" N TYR A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 374 No H-bonds generated for 'chain 'A' and resid 371 through 374' Processing helix chain 'A' and resid 380 through 407 Processing helix chain 'A' and resid 412 through 436 removed outlier: 3.635A pdb=" N SER A 424 " --> pdb=" O MET A 420 " (cutoff:3.500A) Proline residue: A 426 - end of helix Processing helix chain 'A' and resid 442 through 465 Processing helix chain 'A' and resid 470 through 473 No H-bonds generated for 'chain 'A' and resid 470 through 473' Processing helix chain 'A' and resid 513 through 517 Processing helix chain 'A' and resid 523 through 545 removed outlier: 4.298A pdb=" N GLY A 527 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA A 528 " --> pdb=" O TYR A 525 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR A 531 " --> pdb=" O ALA A 528 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU A 532 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N CYS A 537 " --> pdb=" O THR A 534 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLY A 538 " --> pdb=" O MET A 535 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE A 541 " --> pdb=" O GLY A 538 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR A 545 " --> pdb=" O SER A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 552 No H-bonds generated for 'chain 'A' and resid 550 through 552' 260 hydrogen bonds defined for protein. 690 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: 1.02 Time building geometry restraints manager: 1.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 585 1.32 - 1.45: 1036 1.45 - 1.57: 2204 1.57 - 1.69: 2 1.69 - 1.81: 45 Bond restraints: 3872 Sorted by residual: bond pdb=" O12 REO A 702 " pdb="RE REO A 702 " ideal model delta sigma weight residual 2.000 1.735 0.265 2.00e-02 2.50e+03 1.76e+02 bond pdb=" O14 3PH A 703 " pdb=" P 3PH A 703 " ideal model delta sigma weight residual 1.527 1.654 -0.127 2.00e-02 2.50e+03 4.00e+01 bond pdb=" O11 3PH A 703 " pdb=" P 3PH A 703 " ideal model delta sigma weight residual 1.703 1.643 0.060 2.00e-02 2.50e+03 8.88e+00 bond pdb=" O12 3PH A 703 " pdb=" P 3PH A 703 " ideal model delta sigma weight residual 1.526 1.491 0.035 2.00e-02 2.50e+03 3.08e+00 bond pdb=" O13 3PH A 703 " pdb=" P 3PH A 703 " ideal model delta sigma weight residual 1.522 1.491 0.031 2.00e-02 2.50e+03 2.35e+00 ... (remaining 3867 not shown) Histogram of bond angle deviations from ideal: 99.71 - 106.58: 127 106.58 - 113.45: 2168 113.45 - 120.33: 1469 120.33 - 127.20: 1469 127.20 - 134.07: 49 Bond angle restraints: 5282 Sorted by residual: angle pdb=" O12 3PH A 703 " pdb=" P 3PH A 703 " pdb=" O14 3PH A 703 " ideal model delta sigma weight residual 113.84 104.72 9.12 3.00e+00 1.11e-01 9.23e+00 angle pdb=" O12 3PH A 703 " pdb=" P 3PH A 703 " pdb=" O13 3PH A 703 " ideal model delta sigma weight residual 115.12 123.73 -8.61 3.00e+00 1.11e-01 8.23e+00 angle pdb=" O13 3PH A 703 " pdb=" P 3PH A 703 " pdb=" O14 3PH A 703 " ideal model delta sigma weight residual 115.01 109.59 5.42 3.00e+00 1.11e-01 3.27e+00 angle pdb=" CA TYR A 269 " pdb=" CB TYR A 269 " pdb=" CG TYR A 269 " ideal model delta sigma weight residual 113.90 117.11 -3.21 1.80e+00 3.09e-01 3.18e+00 angle pdb=" O11 3PH A 703 " pdb=" P 3PH A 703 " pdb=" O12 3PH A 703 " ideal model delta sigma weight residual 105.09 110.06 -4.97 3.00e+00 1.11e-01 2.75e+00 ... (remaining 5277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 2046 17.48 - 34.96: 137 34.96 - 52.44: 43 52.44 - 69.92: 5 69.92 - 87.40: 2 Dihedral angle restraints: 2233 sinusoidal: 819 harmonic: 1414 Sorted by residual: dihedral pdb=" CA PRO A 555 " pdb=" C PRO A 555 " pdb=" N GLY A 556 " pdb=" CA GLY A 556 " ideal model delta harmonic sigma weight residual 180.00 162.45 17.55 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA TYR A 83 " pdb=" C TYR A 83 " pdb=" N GLY A 84 " pdb=" CA GLY A 84 " ideal model delta harmonic sigma weight residual 180.00 164.28 15.72 0 5.00e+00 4.00e-02 9.88e+00 dihedral pdb=" CB MET A 258 " pdb=" CG MET A 258 " pdb=" SD MET A 258 " pdb=" CE MET A 258 " ideal model delta sinusoidal sigma weight residual 60.00 2.21 57.79 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 2230 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 500 0.041 - 0.082: 112 0.082 - 0.123: 23 0.123 - 0.165: 0 0.165 - 0.206: 1 Chirality restraints: 636 Sorted by residual: chirality pdb=" C2 3PH A 703 " pdb=" C1 3PH A 703 " pdb=" C3 3PH A 703 " pdb=" O21 3PH A 703 " both_signs ideal model delta sigma weight residual False -2.33 -2.53 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ILE A 229 " pdb=" N ILE A 229 " pdb=" C ILE A 229 " pdb=" CB ILE A 229 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.26e-01 chirality pdb=" CB THR A 357 " pdb=" CA THR A 357 " pdb=" OG1 THR A 357 " pdb=" CG2 THR A 357 " both_signs ideal model delta sigma weight residual False 2.55 2.45 0.10 2.00e-01 2.50e+01 2.63e-01 ... (remaining 633 not shown) Planarity restraints: 636 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 101 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.95e+00 pdb=" C THR A 101 " -0.030 2.00e-02 2.50e+03 pdb=" O THR A 101 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA A 102 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 99 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" C LEU A 99 " 0.029 2.00e-02 2.50e+03 pdb=" O LEU A 99 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU A 100 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 98 " 0.008 2.00e-02 2.50e+03 1.55e-02 2.41e+00 pdb=" C SER A 98 " -0.027 2.00e-02 2.50e+03 pdb=" O SER A 98 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU A 99 " 0.009 2.00e-02 2.50e+03 ... (remaining 633 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 262 2.73 - 3.27: 4252 3.27 - 3.81: 6798 3.81 - 4.36: 7975 4.36 - 4.90: 13833 Nonbonded interactions: 33120 Sorted by model distance: nonbonded pdb=" OE1 GLU A 122 " pdb=" NH1 ARG A 130 " model vdw 2.186 2.520 nonbonded pdb=" O LYS A 549 " pdb=" OG SER A 552 " model vdw 2.234 2.440 nonbonded pdb=" OH TYR A 110 " pdb=" N THR A 274 " model vdw 2.240 2.520 nonbonded pdb=" OH TYR A 307 " pdb=" OD2 ASP A 331 " model vdw 2.325 2.440 nonbonded pdb=" NH2 ARG A 241 " pdb=" OE1 GLN A 414 " model vdw 2.349 2.520 ... (remaining 33115 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.110 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.620 Find NCS groups from input model: 0.100 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 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 : 0.006 0.265 3872 Z= 0.388 Angle : 0.570 9.115 5282 Z= 0.282 Chirality : 0.035 0.206 636 Planarity : 0.004 0.038 636 Dihedral : 13.544 87.401 1339 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.51 % Allowed : 9.16 % Favored : 90.33 % 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: 1.14 (0.40), residues: 493 helix: 1.42 (0.27), residues: 388 sheet: None (None), residues: 0 loop : -1.71 (0.65), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 165 HIS 0.001 0.000 HIS A 226 PHE 0.010 0.001 PHE A 304 TYR 0.009 0.001 TYR A 118 ARG 0.001 0.000 ARG A 228 *********************** 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 64 residues out of total 394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 0.440 Fit side-chains REVERT: A 308 LYS cc_start: 0.7338 (ptmm) cc_final: 0.7124 (ptmm) outliers start: 2 outliers final: 2 residues processed: 62 average time/residue: 0.1509 time to fit residues: 11.8786 Evaluate side-chains 60 residues out of total 394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 542 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 12 optimal weight: 0.0980 chunk 25 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 0.0370 chunk 23 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 GLN A 225 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.0842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3872 Z= 0.189 Angle : 0.564 7.182 5282 Z= 0.277 Chirality : 0.038 0.147 636 Planarity : 0.004 0.042 636 Dihedral : 7.543 56.271 575 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.53 % Allowed : 11.70 % Favored : 86.77 % 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: 1.19 (0.40), residues: 493 helix: 1.44 (0.27), residues: 384 sheet: None (None), residues: 0 loop : -1.53 (0.65), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 165 HIS 0.000 0.000 HIS A 273 PHE 0.013 0.001 PHE A 304 TYR 0.013 0.001 TYR A 118 ARG 0.001 0.000 ARG A 228 *********************** 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 75 residues out of total 394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.412 Fit side-chains REVERT: A 232 MET cc_start: 0.7717 (mmm) cc_final: 0.7202 (mmm) REVERT: A 239 ARG cc_start: 0.8114 (mtm180) cc_final: 0.7647 (mtm180) REVERT: A 308 LYS cc_start: 0.7321 (ptmm) cc_final: 0.7023 (ptmm) outliers start: 6 outliers final: 2 residues processed: 74 average time/residue: 0.1357 time to fit residues: 13.0439 Evaluate side-chains 64 residues out of total 394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 104 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 37 optimal weight: 0.0670 chunk 30 optimal weight: 0.4980 chunk 12 optimal weight: 0.0980 chunk 45 optimal weight: 4.9990 chunk 49 optimal weight: 0.0000 chunk 40 optimal weight: 0.8980 chunk 15 optimal weight: 0.1980 chunk 36 optimal weight: 0.6980 chunk 44 optimal weight: 0.3980 overall best weight: 0.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3872 Z= 0.150 Angle : 0.534 6.683 5282 Z= 0.259 Chirality : 0.036 0.144 636 Planarity : 0.004 0.043 636 Dihedral : 7.265 51.829 573 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.04 % Allowed : 14.76 % Favored : 83.21 % 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: 1.44 (0.40), residues: 493 helix: 1.62 (0.27), residues: 384 sheet: None (None), residues: 0 loop : -1.46 (0.64), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 89 HIS 0.000 0.000 HIS A 226 PHE 0.016 0.001 PHE A 304 TYR 0.011 0.001 TYR A 118 ARG 0.001 0.000 ARG A 228 *********************** 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 78 residues out of total 394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 0.378 Fit side-chains REVERT: A 12 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.6908 (m-10) REVERT: A 110 TYR cc_start: 0.7568 (OUTLIER) cc_final: 0.5985 (m-80) REVERT: A 239 ARG cc_start: 0.8069 (mtm180) cc_final: 0.7450 (mtm180) REVERT: A 308 LYS cc_start: 0.7315 (ptmm) cc_final: 0.7073 (ptmm) outliers start: 8 outliers final: 1 residues processed: 77 average time/residue: 0.1408 time to fit residues: 13.8546 Evaluate side-chains 66 residues out of total 394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 110 TYR Chi-restraints excluded: chain A residue 285 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 30 optimal weight: 0.1980 chunk 45 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 43 optimal weight: 0.0050 chunk 13 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3872 Z= 0.210 Angle : 0.568 8.691 5282 Z= 0.273 Chirality : 0.038 0.157 636 Planarity : 0.004 0.047 636 Dihedral : 7.217 54.018 573 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.80 % Allowed : 14.76 % Favored : 82.44 % 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: 1.33 (0.39), residues: 493 helix: 1.53 (0.27), residues: 384 sheet: None (None), residues: 0 loop : -1.42 (0.64), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 165 HIS 0.000 0.000 HIS A 226 PHE 0.017 0.002 PHE A 333 TYR 0.011 0.001 TYR A 118 ARG 0.002 0.000 ARG A 208 *********************** 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 79 residues out of total 394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 68 time to evaluate : 0.400 Fit side-chains REVERT: A 12 PHE cc_start: 0.7768 (OUTLIER) cc_final: 0.6714 (m-10) REVERT: A 232 MET cc_start: 0.7350 (mmm) cc_final: 0.7075 (mmm) REVERT: A 239 ARG cc_start: 0.8082 (mtm180) cc_final: 0.7441 (mtm180) REVERT: A 308 LYS cc_start: 0.7339 (ptmm) cc_final: 0.7016 (ptmm) outliers start: 11 outliers final: 7 residues processed: 76 average time/residue: 0.1284 time to fit residues: 12.6888 Evaluate side-chains 72 residues out of total 394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 553 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 33 optimal weight: 0.1980 chunk 24 optimal weight: 0.0870 chunk 43 optimal weight: 0.9980 chunk 12 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3872 Z= 0.187 Angle : 0.555 7.696 5282 Z= 0.267 Chirality : 0.037 0.155 636 Planarity : 0.004 0.047 636 Dihedral : 7.194 53.716 573 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.82 % Allowed : 14.25 % Favored : 81.93 % 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: 1.30 (0.39), residues: 493 helix: 1.50 (0.27), residues: 385 sheet: None (None), residues: 0 loop : -1.40 (0.64), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 165 HIS 0.000 0.000 HIS A 273 PHE 0.021 0.002 PHE A 193 TYR 0.010 0.001 TYR A 118 ARG 0.001 0.000 ARG A 208 *********************** 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 85 residues out of total 394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 70 time to evaluate : 0.498 Fit side-chains REVERT: A 12 PHE cc_start: 0.7703 (OUTLIER) cc_final: 0.6606 (m-10) REVERT: A 232 MET cc_start: 0.7312 (mmm) cc_final: 0.7060 (mmm) REVERT: A 239 ARG cc_start: 0.8037 (mtm180) cc_final: 0.7418 (mtm180) REVERT: A 308 LYS cc_start: 0.7240 (ptmm) cc_final: 0.6934 (ptmm) REVERT: A 311 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7823 (t70) outliers start: 15 outliers final: 5 residues processed: 80 average time/residue: 0.1393 time to fit residues: 14.2555 Evaluate side-chains 73 residues out of total 394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 553 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 0.8980 chunk 48 optimal weight: 0.2980 chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 chunk 35 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3872 Z= 0.211 Angle : 0.609 13.954 5282 Z= 0.283 Chirality : 0.038 0.175 636 Planarity : 0.004 0.048 636 Dihedral : 7.208 54.881 573 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 4.07 % Allowed : 14.50 % Favored : 81.42 % 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: 1.22 (0.39), residues: 493 helix: 1.44 (0.27), residues: 384 sheet: None (None), residues: 0 loop : -1.40 (0.64), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 559 HIS 0.000 0.000 HIS A 273 PHE 0.024 0.002 PHE A 193 TYR 0.010 0.001 TYR A 118 ARG 0.002 0.000 ARG A 130 *********************** 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 87 residues out of total 394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 71 time to evaluate : 0.356 Fit side-chains REVERT: A 12 PHE cc_start: 0.7704 (OUTLIER) cc_final: 0.6421 (m-10) REVERT: A 89 TRP cc_start: 0.8283 (m100) cc_final: 0.8040 (m100) REVERT: A 232 MET cc_start: 0.7271 (mmm) cc_final: 0.7065 (mmm) REVERT: A 239 ARG cc_start: 0.8069 (mtm180) cc_final: 0.7436 (mtm180) REVERT: A 308 LYS cc_start: 0.7258 (ptmm) cc_final: 0.6955 (ptmm) REVERT: A 311 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7955 (t70) REVERT: A 339 VAL cc_start: 0.7841 (OUTLIER) cc_final: 0.7624 (m) outliers start: 16 outliers final: 8 residues processed: 82 average time/residue: 0.1273 time to fit residues: 13.5642 Evaluate side-chains 79 residues out of total 394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 68 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 553 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 30 optimal weight: 0.1980 chunk 29 optimal weight: 0.0370 chunk 22 optimal weight: 0.2980 chunk 19 optimal weight: 0.7980 chunk 28 optimal weight: 0.0870 chunk 14 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.2436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3872 Z= 0.157 Angle : 0.570 11.178 5282 Z= 0.269 Chirality : 0.036 0.136 636 Planarity : 0.004 0.048 636 Dihedral : 7.138 50.048 573 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.56 % Allowed : 15.01 % Favored : 81.42 % 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: 1.33 (0.39), residues: 493 helix: 1.51 (0.27), residues: 385 sheet: None (None), residues: 0 loop : -1.34 (0.65), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 559 HIS 0.000 0.000 HIS A 273 PHE 0.016 0.001 PHE A 304 TYR 0.010 0.001 TYR A 118 ARG 0.001 0.000 ARG A 130 *********************** 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 84 residues out of total 394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 70 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 12 PHE cc_start: 0.7528 (OUTLIER) cc_final: 0.6465 (m-10) REVERT: A 232 MET cc_start: 0.7201 (mmm) cc_final: 0.6987 (mmm) REVERT: A 308 LYS cc_start: 0.7231 (ptmm) cc_final: 0.6933 (ptmm) REVERT: A 311 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7985 (t70) REVERT: A 339 VAL cc_start: 0.7766 (OUTLIER) cc_final: 0.7561 (m) outliers start: 14 outliers final: 7 residues processed: 80 average time/residue: 0.1320 time to fit residues: 13.8796 Evaluate side-chains 79 residues out of total 394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 69 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 553 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 0.1980 chunk 46 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 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 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3872 Z= 0.258 Angle : 0.606 10.021 5282 Z= 0.290 Chirality : 0.039 0.187 636 Planarity : 0.005 0.049 636 Dihedral : 7.256 57.937 573 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.05 % Allowed : 15.78 % Favored : 81.17 % 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: 1.18 (0.39), residues: 493 helix: 1.34 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -0.99 (0.63), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 559 HIS 0.000 0.000 HIS A 226 PHE 0.017 0.002 PHE A 193 TYR 0.010 0.002 TYR A 324 ARG 0.001 0.000 ARG A 111 *********************** 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 78 residues out of total 394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 66 time to evaluate : 0.402 Fit side-chains REVERT: A 12 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.6575 (m-10) REVERT: A 176 THR cc_start: 0.7399 (p) cc_final: 0.7099 (p) REVERT: A 232 MET cc_start: 0.7310 (mmm) cc_final: 0.7102 (mmm) REVERT: A 239 ARG cc_start: 0.8101 (mtm180) cc_final: 0.7481 (mtm180) REVERT: A 308 LYS cc_start: 0.7255 (ptmm) cc_final: 0.6961 (ptmm) REVERT: A 311 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.8113 (t70) outliers start: 12 outliers final: 6 residues processed: 75 average time/residue: 0.1054 time to fit residues: 10.8689 Evaluate side-chains 73 residues out of total 394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 553 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 0.0370 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 0.4980 chunk 22 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 45 optimal weight: 0.0470 chunk 39 optimal weight: 0.5980 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3872 Z= 0.176 Angle : 0.574 9.588 5282 Z= 0.274 Chirality : 0.037 0.145 636 Planarity : 0.004 0.048 636 Dihedral : 7.177 52.680 573 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.04 % Allowed : 16.79 % Favored : 81.17 % 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: 1.27 (0.39), residues: 493 helix: 1.42 (0.27), residues: 379 sheet: None (None), residues: 0 loop : -1.05 (0.62), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 559 HIS 0.001 0.000 HIS A 273 PHE 0.016 0.001 PHE A 304 TYR 0.010 0.001 TYR A 118 ARG 0.001 0.000 ARG A 130 *********************** 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 78 residues out of total 394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 0.375 Fit side-chains REVERT: A 12 PHE cc_start: 0.7615 (OUTLIER) cc_final: 0.6511 (m-10) REVERT: A 232 MET cc_start: 0.7234 (mmm) cc_final: 0.7033 (mmm) REVERT: A 239 ARG cc_start: 0.8030 (mtm180) cc_final: 0.7403 (mtm180) REVERT: A 308 LYS cc_start: 0.7242 (ptmm) cc_final: 0.6966 (ptmm) REVERT: A 311 ASP cc_start: 0.8277 (OUTLIER) cc_final: 0.8057 (t70) outliers start: 8 outliers final: 5 residues processed: 76 average time/residue: 0.1376 time to fit residues: 13.7118 Evaluate side-chains 75 residues out of total 394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 68 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 553 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.6980 chunk 30 optimal weight: 0.0010 chunk 24 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3872 Z= 0.210 Angle : 0.590 9.236 5282 Z= 0.280 Chirality : 0.038 0.189 636 Planarity : 0.005 0.049 636 Dihedral : 7.190 54.133 573 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.29 % Allowed : 16.28 % Favored : 81.42 % 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: 1.25 (0.39), residues: 493 helix: 1.36 (0.27), residues: 385 sheet: None (None), residues: 0 loop : -0.98 (0.66), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 559 HIS 0.000 0.000 HIS A 273 PHE 0.020 0.002 PHE A 193 TYR 0.010 0.001 TYR A 118 ARG 0.002 0.000 ARG A 130 ********************** 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 76 residues out of total 394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 67 time to evaluate : 0.415 Fit side-chains REVERT: A 12 PHE cc_start: 0.7600 (OUTLIER) cc_final: 0.6520 (m-10) REVERT: A 239 ARG cc_start: 0.8031 (mtm180) cc_final: 0.7405 (mtm180) REVERT: A 308 LYS cc_start: 0.7416 (ptmm) cc_final: 0.7124 (ptmm) REVERT: A 311 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.8071 (t70) outliers start: 9 outliers final: 7 residues processed: 74 average time/residue: 0.1174 time to fit residues: 11.6448 Evaluate side-chains 76 residues out of total 394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 67 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 553 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 2 optimal weight: 0.0970 chunk 28 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.186595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.160922 restraints weight = 2803.653| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 1.10 r_work: 0.3599 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3872 Z= 0.233 Angle : 0.648 15.546 5282 Z= 0.297 Chirality : 0.038 0.144 636 Planarity : 0.005 0.049 636 Dihedral : 7.229 55.311 573 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.04 % Allowed : 17.30 % Favored : 80.66 % 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: 1.19 (0.39), residues: 493 helix: 1.36 (0.27), residues: 383 sheet: None (None), residues: 0 loop : -1.13 (0.64), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 559 HIS 0.000 0.000 HIS A 273 PHE 0.014 0.002 PHE A 304 TYR 0.010 0.001 TYR A 118 ARG 0.001 0.000 ARG A 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1260.81 seconds wall clock time: 23 minutes 19.51 seconds (1399.51 seconds total)