Starting phenix.real_space_refine on Wed Jun 4 23:55:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fh0_50435/06_2025/9fh0_50435.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fh0_50435/06_2025/9fh0_50435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fh0_50435/06_2025/9fh0_50435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fh0_50435/06_2025/9fh0_50435.map" model { file = "/net/cci-nas-00/data/ceres_data/9fh0_50435/06_2025/9fh0_50435.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fh0_50435/06_2025/9fh0_50435.cif" } resolution = 2.9 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= 0.023 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: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 2893 2.51 5 N 760 2.21 5 O 825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 4503 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2152 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 261} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2351 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 8, 'TRANS': 304} Chain breaks: 2 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 6, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 97 Time building chain proxies: 4.08, per 1000 atoms: 0.91 Number of scatterers: 4503 At special positions: 0 Unit cell: (79.148, 66.518, 95.146, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 25 16.00 O 825 8.00 N 760 7.00 C 2893 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: 1.14 Conformation dependent library (CDL) restraints added in 553.3 milliseconds 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1106 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 2 sheets defined 65.8% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 26 through 30 Processing helix chain 'A' and resid 34 through 49 Processing helix chain 'A' and resid 88 through 110 removed outlier: 4.695A pdb=" N ALA A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ARG A 100 " --> pdb=" O ASN A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 132 Processing helix chain 'A' and resid 149 through 154 Processing helix chain 'A' and resid 160 through 170 Proline residue: A 166 - end of helix Processing helix chain 'A' and resid 170 through 180 removed outlier: 3.828A pdb=" N PHE A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 192 Processing helix chain 'A' and resid 205 through 221 removed outlier: 3.665A pdb=" N PHE A 209 " --> pdb=" O ASN A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 238 removed outlier: 3.671A pdb=" N CYS A 229 " --> pdb=" O TYR A 225 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER A 238 " --> pdb=" O LYS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 255 removed outlier: 3.719A pdb=" N ASN A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 262 removed outlier: 3.676A pdb=" N GLY A 262 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 272 Processing helix chain 'G' and resid 291 through 296 removed outlier: 4.829A pdb=" N ASN G 296 " --> pdb=" O GLY G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 314 through 325 Processing helix chain 'G' and resid 328 through 343 removed outlier: 3.519A pdb=" N ALA G 332 " --> pdb=" O LYS G 328 " (cutoff:3.500A) Processing helix chain 'G' and resid 346 through 360 Processing helix chain 'G' and resid 362 through 377 Processing helix chain 'G' and resid 380 through 395 removed outlier: 3.921A pdb=" N MET G 384 " --> pdb=" O ASN G 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 396 through 412 Processing helix chain 'G' and resid 412 through 421 Processing helix chain 'G' and resid 436 through 451 Processing helix chain 'G' and resid 459 through 471 Processing helix chain 'G' and resid 472 through 486 removed outlier: 3.755A pdb=" N THR G 476 " --> pdb=" O ASP G 472 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL G 486 " --> pdb=" O SER G 482 " (cutoff:3.500A) Processing helix chain 'G' and resid 491 through 504 Processing helix chain 'G' and resid 506 through 521 Processing helix chain 'G' and resid 524 through 538 removed outlier: 3.585A pdb=" N ARG G 528 " --> pdb=" O PHE G 524 " (cutoff:3.500A) Processing helix chain 'G' and resid 541 through 556 Processing helix chain 'G' and resid 578 through 589 removed outlier: 3.593A pdb=" N MET G 588 " --> pdb=" O VAL G 584 " (cutoff:3.500A) Processing helix chain 'G' and resid 590 through 595 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 16 removed outlier: 4.050A pdb=" N LYS A 197 " --> pdb=" O VAL A 137 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 123 through 124 removed outlier: 6.764A pdb=" N ALA A 123 " --> pdb=" O LEU A 147 " (cutoff:3.500A) 270 hydrogen bonds defined for protein. 795 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.26 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1057 1.33 - 1.45: 928 1.45 - 1.57: 2568 1.57 - 1.69: 0 1.69 - 1.81: 39 Bond restraints: 4592 Sorted by residual: bond pdb=" CB ILE A 21 " pdb=" CG2 ILE A 21 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.69e+00 bond pdb=" CB ASN A 120 " pdb=" CG ASN A 120 " ideal model delta sigma weight residual 1.516 1.469 0.047 2.50e-02 1.60e+03 3.46e+00 bond pdb=" CB VAL A 163 " pdb=" CG2 VAL A 163 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.43e+00 bond pdb=" CG LYS A 233 " pdb=" CD LYS A 233 " ideal model delta sigma weight residual 1.520 1.469 0.051 3.00e-02 1.11e+03 2.94e+00 bond pdb=" CG LEU A 45 " pdb=" CD2 LEU A 45 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.87e+00 ... (remaining 4587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 5770 1.47 - 2.94: 385 2.94 - 4.41: 38 4.41 - 5.88: 15 5.88 - 7.35: 8 Bond angle restraints: 6216 Sorted by residual: angle pdb=" C GLU A 251 " pdb=" N VAL A 252 " pdb=" CA VAL A 252 " ideal model delta sigma weight residual 120.64 116.07 4.57 1.66e+00 3.63e-01 7.57e+00 angle pdb=" C ARG A 269 " pdb=" N GLN A 270 " pdb=" CA GLN A 270 " ideal model delta sigma weight residual 121.94 116.69 5.25 2.00e+00 2.50e-01 6.89e+00 angle pdb=" C SER A 164 " pdb=" N LEU A 165 " pdb=" CA LEU A 165 " ideal model delta sigma weight residual 121.80 115.56 6.24 2.44e+00 1.68e-01 6.54e+00 angle pdb=" C ASP G 490 " pdb=" N GLU G 491 " pdb=" CA GLU G 491 " ideal model delta sigma weight residual 122.79 118.24 4.55 1.78e+00 3.16e-01 6.53e+00 angle pdb=" C ASN G 360 " pdb=" N GLU G 361 " pdb=" CA GLU G 361 " ideal model delta sigma weight residual 122.74 126.25 -3.51 1.44e+00 4.82e-01 5.94e+00 ... (remaining 6211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 2490 17.38 - 34.76: 207 34.76 - 52.14: 40 52.14 - 69.52: 9 69.52 - 86.90: 2 Dihedral angle restraints: 2748 sinusoidal: 1037 harmonic: 1711 Sorted by residual: dihedral pdb=" CA THR G 576 " pdb=" C THR G 576 " pdb=" N VAL G 577 " pdb=" CA VAL G 577 " ideal model delta harmonic sigma weight residual -180.00 -156.76 -23.24 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA TYR G 287 " pdb=" C TYR G 287 " pdb=" N LEU G 288 " pdb=" CA LEU G 288 " ideal model delta harmonic sigma weight residual 180.00 157.07 22.93 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA ASP G 279 " pdb=" C ASP G 279 " pdb=" N ASP G 280 " pdb=" CA ASP G 280 " ideal model delta harmonic sigma weight residual 180.00 157.98 22.02 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 2745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 366 0.041 - 0.082: 238 0.082 - 0.123: 81 0.123 - 0.163: 14 0.163 - 0.204: 2 Chirality restraints: 701 Sorted by residual: chirality pdb=" CB ILE G 538 " pdb=" CA ILE G 538 " pdb=" CG1 ILE G 538 " pdb=" CG2 ILE G 538 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA SER A 238 " pdb=" N SER A 238 " pdb=" C SER A 238 " pdb=" CB SER A 238 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.03e-01 chirality pdb=" CB ILE A 241 " pdb=" CA ILE A 241 " pdb=" CG1 ILE A 241 " pdb=" CG2 ILE A 241 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.57e-01 ... (remaining 698 not shown) Planarity restraints: 797 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 94 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.61e+00 pdb=" C VAL A 94 " 0.037 2.00e-02 2.50e+03 pdb=" O VAL A 94 " -0.014 2.00e-02 2.50e+03 pdb=" N SER A 95 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 182 " 0.028 5.00e-02 4.00e+02 4.21e-02 2.84e+00 pdb=" N PRO A 183 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 183 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 183 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 121 " -0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO A 122 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 122 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 122 " -0.022 5.00e-02 4.00e+02 ... (remaining 794 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 94 2.68 - 3.23: 4387 3.23 - 3.79: 6924 3.79 - 4.34: 9598 4.34 - 4.90: 15917 Nonbonded interactions: 36920 Sorted by model distance: nonbonded pdb=" OH TYR G 316 " pdb=" OD2 ASP G 348 " model vdw 2.121 3.040 nonbonded pdb=" OD1 ASP A 49 " pdb=" OG SER A 112 " model vdw 2.133 3.040 nonbonded pdb=" O GLY G 608 " pdb=" OG SER G 611 " model vdw 2.139 3.040 nonbonded pdb=" OG1 THR A 162 " pdb=" OE2 GLU A 251 " model vdw 2.202 3.040 nonbonded pdb=" NH1 ARG A 14 " pdb=" OE2 GLU A 16 " model vdw 2.216 3.120 ... (remaining 36915 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.710 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 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 : 0.013 0.083 4592 Z= 0.540 Angle : 0.828 7.345 6216 Z= 0.440 Chirality : 0.055 0.204 701 Planarity : 0.005 0.042 797 Dihedral : 13.667 86.901 1642 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % 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: -3.02 (0.29), residues: 575 helix: -1.33 (0.24), residues: 369 sheet: -1.21 (0.83), residues: 30 loop : -3.39 (0.35), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 407 HIS 0.006 0.002 HIS G 346 PHE 0.020 0.003 PHE G 524 TYR 0.012 0.002 TYR G 468 ARG 0.008 0.001 ARG G 526 Details of bonding type rmsd hydrogen bonds : bond 0.15431 ( 270) hydrogen bonds : angle 5.84489 ( 795) covalent geometry : bond 0.01316 ( 4592) covalent geometry : angle 0.82817 ( 6216) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.546 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 1.7211 time to fit residues: 97.5650 Evaluate side-chains 36 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 23 optimal weight: 0.0670 chunk 45 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 101 ASN A 181 ASN A 278 HIS G 278 ASN G 312 ASN ** G 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 GLN G 444 GLN G 447 GLN ** G 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 503 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.123857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.081751 restraints weight = 6675.790| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.57 r_work: 0.2831 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4592 Z= 0.130 Angle : 0.524 5.513 6216 Z= 0.277 Chirality : 0.041 0.176 701 Planarity : 0.004 0.040 797 Dihedral : 4.803 21.860 626 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.75 % Allowed : 9.85 % Favored : 88.40 % 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: -0.83 (0.33), residues: 575 helix: 0.39 (0.27), residues: 361 sheet: -0.43 (0.85), residues: 33 loop : -2.47 (0.39), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 93 HIS 0.005 0.001 HIS G 346 PHE 0.015 0.001 PHE G 310 TYR 0.010 0.001 TYR G 468 ARG 0.006 0.000 ARG G 352 Details of bonding type rmsd hydrogen bonds : bond 0.04060 ( 270) hydrogen bonds : angle 4.27352 ( 795) covalent geometry : bond 0.00303 ( 4592) covalent geometry : angle 0.52443 ( 6216) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.524 Fit side-chains REVERT: A 215 GLU cc_start: 0.8157 (tp30) cc_final: 0.7902 (tp30) outliers start: 8 outliers final: 0 residues processed: 50 average time/residue: 1.5161 time to fit residues: 78.4006 Evaluate side-chains 38 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 38 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 17 optimal weight: 0.2980 chunk 42 optimal weight: 10.0000 chunk 44 optimal weight: 0.0970 chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 346 HIS G 422 GLN G 444 GLN ** G 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.125646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.083916 restraints weight = 6643.924| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.57 r_work: 0.2863 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4592 Z= 0.106 Angle : 0.492 9.996 6216 Z= 0.255 Chirality : 0.040 0.180 701 Planarity : 0.003 0.035 797 Dihedral : 4.294 19.952 626 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.31 % Allowed : 14.66 % Favored : 84.03 % 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: 0.34 (0.35), residues: 575 helix: 1.30 (0.28), residues: 363 sheet: -0.09 (0.84), residues: 33 loop : -2.00 (0.42), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 93 HIS 0.002 0.001 HIS G 346 PHE 0.013 0.001 PHE G 310 TYR 0.007 0.001 TYR G 468 ARG 0.004 0.000 ARG G 418 Details of bonding type rmsd hydrogen bonds : bond 0.03410 ( 270) hydrogen bonds : angle 3.87286 ( 795) covalent geometry : bond 0.00240 ( 4592) covalent geometry : angle 0.49181 ( 6216) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.488 Fit side-chains REVERT: A 215 GLU cc_start: 0.8138 (tp30) cc_final: 0.7838 (tp30) outliers start: 6 outliers final: 1 residues processed: 55 average time/residue: 1.4199 time to fit residues: 80.8977 Evaluate side-chains 42 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 405 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 6 optimal weight: 0.1980 chunk 10 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN A 275 GLN ** G 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.125387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.082821 restraints weight = 6678.881| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 1.61 r_work: 0.2833 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4592 Z= 0.147 Angle : 0.502 8.877 6216 Z= 0.261 Chirality : 0.041 0.192 701 Planarity : 0.003 0.034 797 Dihedral : 4.298 19.317 626 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.09 % Allowed : 15.10 % Favored : 83.81 % 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: 0.66 (0.36), residues: 575 helix: 1.48 (0.28), residues: 364 sheet: -0.06 (0.84), residues: 33 loop : -1.70 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 93 HIS 0.001 0.000 HIS G 346 PHE 0.011 0.001 PHE A 97 TYR 0.015 0.001 TYR G 316 ARG 0.003 0.000 ARG A 269 Details of bonding type rmsd hydrogen bonds : bond 0.03839 ( 270) hydrogen bonds : angle 3.87811 ( 795) covalent geometry : bond 0.00356 ( 4592) covalent geometry : angle 0.50192 ( 6216) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.520 Fit side-chains REVERT: A 215 GLU cc_start: 0.8173 (tp30) cc_final: 0.7838 (tp30) REVERT: A 232 MET cc_start: 0.9268 (mtm) cc_final: 0.9057 (mtm) outliers start: 5 outliers final: 0 residues processed: 44 average time/residue: 1.4700 time to fit residues: 67.1841 Evaluate side-chains 42 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 43 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 17 optimal weight: 0.5980 chunk 7 optimal weight: 0.0270 chunk 38 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN A 270 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.125726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.083866 restraints weight = 6784.707| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.63 r_work: 0.2842 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4592 Z= 0.102 Angle : 0.453 8.588 6216 Z= 0.237 Chirality : 0.039 0.192 701 Planarity : 0.003 0.036 797 Dihedral : 4.106 18.914 626 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.53 % Allowed : 15.75 % Favored : 82.71 % 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: 0.94 (0.36), residues: 575 helix: 1.74 (0.28), residues: 364 sheet: 0.11 (0.85), residues: 33 loop : -1.68 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 93 HIS 0.001 0.000 HIS G 440 PHE 0.009 0.001 PHE A 97 TYR 0.008 0.001 TYR G 316 ARG 0.003 0.000 ARG A 269 Details of bonding type rmsd hydrogen bonds : bond 0.03177 ( 270) hydrogen bonds : angle 3.71709 ( 795) covalent geometry : bond 0.00234 ( 4592) covalent geometry : angle 0.45334 ( 6216) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.514 Fit side-chains REVERT: A 215 GLU cc_start: 0.8075 (tp30) cc_final: 0.7714 (tp30) outliers start: 7 outliers final: 1 residues processed: 52 average time/residue: 1.3482 time to fit residues: 72.9163 Evaluate side-chains 45 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 17 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 346 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.123041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.080847 restraints weight = 6711.582| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 1.61 r_work: 0.2803 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 4592 Z= 0.201 Angle : 0.534 7.017 6216 Z= 0.277 Chirality : 0.042 0.163 701 Planarity : 0.004 0.034 797 Dihedral : 4.324 20.642 626 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.09 % Allowed : 16.41 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.36), residues: 575 helix: 1.69 (0.28), residues: 363 sheet: -0.03 (0.85), residues: 33 loop : -1.63 (0.45), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 93 HIS 0.002 0.001 HIS A 23 PHE 0.013 0.001 PHE A 97 TYR 0.011 0.001 TYR G 468 ARG 0.004 0.000 ARG A 269 Details of bonding type rmsd hydrogen bonds : bond 0.04381 ( 270) hydrogen bonds : angle 3.90194 ( 795) covalent geometry : bond 0.00496 ( 4592) covalent geometry : angle 0.53396 ( 6216) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.477 Fit side-chains REVERT: A 215 GLU cc_start: 0.8118 (tp30) cc_final: 0.7736 (tp30) outliers start: 5 outliers final: 3 residues processed: 43 average time/residue: 1.4434 time to fit residues: 64.4360 Evaluate side-chains 40 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain G residue 346 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 28 optimal weight: 0.8980 chunk 26 optimal weight: 0.0070 chunk 51 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN G 346 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.126053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.084179 restraints weight = 6691.707| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.62 r_work: 0.2861 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4592 Z= 0.096 Angle : 0.453 7.002 6216 Z= 0.239 Chirality : 0.039 0.169 701 Planarity : 0.003 0.037 797 Dihedral : 4.113 18.981 626 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.88 % Allowed : 17.07 % Favored : 82.06 % 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: 1.10 (0.36), residues: 575 helix: 1.88 (0.28), residues: 364 sheet: 0.07 (0.85), residues: 33 loop : -1.63 (0.45), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 350 HIS 0.009 0.001 HIS G 346 PHE 0.009 0.001 PHE A 97 TYR 0.007 0.001 TYR G 468 ARG 0.004 0.000 ARG G 352 Details of bonding type rmsd hydrogen bonds : bond 0.03089 ( 270) hydrogen bonds : angle 3.70135 ( 795) covalent geometry : bond 0.00214 ( 4592) covalent geometry : angle 0.45307 ( 6216) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.488 Fit side-chains REVERT: A 215 GLU cc_start: 0.8071 (tp30) cc_final: 0.7715 (tp30) outliers start: 4 outliers final: 3 residues processed: 45 average time/residue: 1.3747 time to fit residues: 64.2502 Evaluate side-chains 45 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain G residue 405 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 23 optimal weight: 0.0980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.124342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.082281 restraints weight = 6632.357| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 1.61 r_work: 0.2838 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 4592 Z= 0.150 Angle : 0.499 7.416 6216 Z= 0.264 Chirality : 0.040 0.154 701 Planarity : 0.003 0.035 797 Dihedral : 4.154 19.582 626 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.66 % Allowed : 16.85 % Favored : 82.49 % 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 (0.36), residues: 575 helix: 1.89 (0.28), residues: 363 sheet: 0.10 (0.86), residues: 33 loop : -1.55 (0.45), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 93 HIS 0.002 0.000 HIS G 346 PHE 0.012 0.001 PHE A 97 TYR 0.011 0.001 TYR G 468 ARG 0.004 0.000 ARG A 269 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 270) hydrogen bonds : angle 3.75574 ( 795) covalent geometry : bond 0.00365 ( 4592) covalent geometry : angle 0.49928 ( 6216) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.498 Fit side-chains REVERT: A 215 GLU cc_start: 0.8100 (tp30) cc_final: 0.7742 (tp30) REVERT: G 310 PHE cc_start: 0.7474 (m-80) cc_final: 0.7187 (m-80) outliers start: 3 outliers final: 3 residues processed: 50 average time/residue: 1.3870 time to fit residues: 71.9590 Evaluate side-chains 42 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain G residue 405 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 7 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 56 optimal weight: 8.9990 chunk 54 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 57 optimal weight: 10.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 346 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.123256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.080954 restraints weight = 6779.188| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 1.64 r_work: 0.2806 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4592 Z= 0.193 Angle : 0.523 6.149 6216 Z= 0.272 Chirality : 0.042 0.149 701 Planarity : 0.004 0.034 797 Dihedral : 4.286 20.857 626 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.88 % Allowed : 17.72 % Favored : 81.40 % 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: 1.04 (0.36), residues: 575 helix: 1.79 (0.28), residues: 364 sheet: -0.00 (0.85), residues: 33 loop : -1.56 (0.45), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 93 HIS 0.002 0.001 HIS A 23 PHE 0.013 0.001 PHE A 97 TYR 0.012 0.001 TYR G 468 ARG 0.004 0.000 ARG A 269 Details of bonding type rmsd hydrogen bonds : bond 0.04232 ( 270) hydrogen bonds : angle 3.87826 ( 795) covalent geometry : bond 0.00475 ( 4592) covalent geometry : angle 0.52313 ( 6216) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.530 Fit side-chains REVERT: A 215 GLU cc_start: 0.8127 (tp30) cc_final: 0.7768 (tp30) REVERT: G 310 PHE cc_start: 0.7544 (m-80) cc_final: 0.7207 (m-80) REVERT: G 471 ASP cc_start: 0.8587 (t0) cc_final: 0.7901 (t0) outliers start: 4 outliers final: 3 residues processed: 42 average time/residue: 1.4895 time to fit residues: 64.9444 Evaluate side-chains 41 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain G residue 346 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 37 optimal weight: 0.9980 chunk 1 optimal weight: 0.0670 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 346 HIS G 519 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.124602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.082372 restraints weight = 6663.861| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.63 r_work: 0.2838 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4592 Z= 0.117 Angle : 0.472 6.178 6216 Z= 0.248 Chirality : 0.039 0.151 701 Planarity : 0.003 0.036 797 Dihedral : 4.180 19.959 626 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.66 % Allowed : 17.94 % Favored : 81.40 % 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: 1.20 (0.36), residues: 575 helix: 1.91 (0.28), residues: 364 sheet: 0.06 (0.85), residues: 33 loop : -1.48 (0.45), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 350 HIS 0.001 0.000 HIS A 23 PHE 0.010 0.001 PHE A 97 TYR 0.010 0.001 TYR G 468 ARG 0.004 0.000 ARG A 269 Details of bonding type rmsd hydrogen bonds : bond 0.03456 ( 270) hydrogen bonds : angle 3.75075 ( 795) covalent geometry : bond 0.00273 ( 4592) covalent geometry : angle 0.47245 ( 6216) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.526 Fit side-chains REVERT: A 215 GLU cc_start: 0.8091 (tp30) cc_final: 0.7726 (tp30) REVERT: G 310 PHE cc_start: 0.7476 (m-80) cc_final: 0.7156 (m-80) REVERT: G 471 ASP cc_start: 0.8519 (t0) cc_final: 0.7935 (t0) outliers start: 3 outliers final: 2 residues processed: 44 average time/residue: 1.5013 time to fit residues: 68.5581 Evaluate side-chains 43 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 265 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 17 optimal weight: 0.4980 chunk 37 optimal weight: 0.5980 chunk 32 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 346 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.124513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.082246 restraints weight = 6669.775| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.63 r_work: 0.2835 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4592 Z= 0.131 Angle : 0.477 6.253 6216 Z= 0.250 Chirality : 0.040 0.149 701 Planarity : 0.003 0.036 797 Dihedral : 4.139 19.823 626 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.66 % Allowed : 17.94 % Favored : 81.40 % 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: 1.24 (0.36), residues: 575 helix: 1.95 (0.28), residues: 364 sheet: 0.01 (0.85), residues: 33 loop : -1.47 (0.45), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 93 HIS 0.001 0.000 HIS A 23 PHE 0.011 0.001 PHE A 97 TYR 0.010 0.001 TYR G 468 ARG 0.004 0.000 ARG A 269 Details of bonding type rmsd hydrogen bonds : bond 0.03564 ( 270) hydrogen bonds : angle 3.73134 ( 795) covalent geometry : bond 0.00315 ( 4592) covalent geometry : angle 0.47743 ( 6216) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3799.50 seconds wall clock time: 65 minutes 28.00 seconds (3928.00 seconds total)