Starting phenix.real_space_refine on Sat May 10 01:46:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dnz_27585/05_2025/8dnz_27585_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dnz_27585/05_2025/8dnz_27585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dnz_27585/05_2025/8dnz_27585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dnz_27585/05_2025/8dnz_27585.map" model { file = "/net/cci-nas-00/data/ceres_data/8dnz_27585/05_2025/8dnz_27585_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dnz_27585/05_2025/8dnz_27585_trim.cif" } resolution = 2.57 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= 0.003 sd= 0.055 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 27 5.16 5 C 2872 2.51 5 N 694 2.21 5 O 744 1.98 5 H 38 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 4375 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 480 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 57} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 251 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain: "A" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3548 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 438} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 96 Unusual residues: {'T69': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'NMTRANS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="T69 D 1 " pdbres="0A1 D 2 " Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'IML:plan-1': 1, 'MAA:plan-1': 2, '0A1:plan-2': 1, 'T69:plan-1': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 3.41, per 1000 atoms: 0.78 Number of scatterers: 4375 At special positions: 0 Unit cell: (93.45, 80.85, 78.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 O 744 8.00 N 694 7.00 C 2872 6.00 H 38 1.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 520.8 milliseconds 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1018 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 4 sheets defined 73.7% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'B' and resid 7 through 25 Processing helix chain 'B' and resid 29 through 66 Proline residue: B 60 - end of helix Processing helix chain 'C' and resid 69 through 96 Processing helix chain 'A' and resid 4 through 9 removed outlier: 3.539A pdb=" N VAL A 8 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 9 " --> pdb=" O PHE A 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4 through 9' Processing helix chain 'A' and resid 9 through 14 Processing helix chain 'A' and resid 27 through 46 Processing helix chain 'A' and resid 62 through 66 removed outlier: 3.577A pdb=" N ARG A 66 " --> pdb=" O TYR A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 97 Processing helix chain 'A' and resid 105 through 134 Processing helix chain 'A' and resid 139 through 144 Processing helix chain 'A' and resid 144 through 171 Processing helix chain 'A' and resid 177 through 197 Processing helix chain 'A' and resid 211 through 223 Processing helix chain 'A' and resid 226 through 235 Processing helix chain 'A' and resid 241 through 260 Processing helix chain 'A' and resid 288 through 312 Processing helix chain 'A' and resid 315 through 322 Processing helix chain 'A' and resid 340 through 345 removed outlier: 3.752A pdb=" N TYR A 344 " --> pdb=" O GLY A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 357 Processing helix chain 'A' and resid 357 through 381 removed outlier: 3.591A pdb=" N ALA A 361 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 398 Processing helix chain 'A' and resid 409 through 438 Proline residue: A 418 - end of helix removed outlier: 3.543A pdb=" N SER A 432 " --> pdb=" O ILE A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 468 removed outlier: 3.583A pdb=" N GLY A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 67 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 200 through 202 Processing sheet with id=AA3, first strand: chain 'A' and resid 276 through 282 Processing sheet with id=AA4, first strand: chain 'A' and resid 323 through 325 removed outlier: 6.477A pdb=" N THR A 323 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR A 336 " --> pdb=" O SER A 325 " (cutoff:3.500A) 316 hydrogen bonds defined for protein. 945 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.18 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.16: 38 1.16 - 1.33: 746 1.33 - 1.49: 1721 1.49 - 1.65: 1916 1.65 - 1.82: 46 Bond restraints: 4467 Sorted by residual: bond pdb=" CD1 0A1 D 2 " pdb=" HD1 0A1 D 2 " ideal model delta sigma weight residual 0.930 1.158 -0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" CE1 0A1 D 2 " pdb=" HE1 0A1 D 2 " ideal model delta sigma weight residual 0.930 1.156 -0.226 2.00e-02 2.50e+03 1.27e+02 bond pdb=" CD2 0A1 D 2 " pdb=" HD2 0A1 D 2 " ideal model delta sigma weight residual 0.930 1.150 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" CE2 0A1 D 2 " pdb=" HE2 0A1 D 2 " ideal model delta sigma weight residual 0.930 1.122 -0.192 2.00e-02 2.50e+03 9.23e+01 bond pdb=" CA MAA D 3 " pdb=" HA MAA D 3 " ideal model delta sigma weight residual 0.970 1.149 -0.179 2.00e-02 2.50e+03 7.98e+01 ... (remaining 4462 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.34: 6042 4.34 - 8.67: 31 8.67 - 13.01: 4 13.01 - 17.34: 1 17.34 - 21.68: 1 Bond angle restraints: 6079 Sorted by residual: angle pdb=" CA MAA D 5 " pdb=" C MAA D 5 " pdb=" O MAA D 5 " ideal model delta sigma weight residual 120.80 107.21 13.59 1.70e+00 3.46e-01 6.39e+01 angle pdb=" C25 T69 D 1 " pdb=" C26 T69 D 1 " pdb=" N12 T69 D 1 " ideal model delta sigma weight residual 111.50 133.18 -21.68 3.00e+00 1.11e-01 5.22e+01 angle pdb=" N GLY A 442 " pdb=" CA GLY A 442 " pdb=" C GLY A 442 " ideal model delta sigma weight residual 113.58 106.52 7.06 1.07e+00 8.73e-01 4.35e+01 angle pdb=" CA 0A1 D 2 " pdb=" C 0A1 D 2 " pdb=" N MAA D 3 " ideal model delta sigma weight residual 116.20 127.09 -10.89 2.00e+00 2.50e-01 2.97e+01 angle pdb=" N 0A1 D 2 " pdb=" CA 0A1 D 2 " pdb=" CB 0A1 D 2 " ideal model delta sigma weight residual 110.50 119.64 -9.14 1.70e+00 3.46e-01 2.89e+01 ... (remaining 6074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 2398 17.01 - 34.02: 215 34.02 - 51.02: 32 51.02 - 68.03: 9 68.03 - 85.04: 6 Dihedral angle restraints: 2660 sinusoidal: 1074 harmonic: 1586 Sorted by residual: dihedral pdb=" CB MET A 77 " pdb=" CG MET A 77 " pdb=" SD MET A 77 " pdb=" CE MET A 77 " ideal model delta sinusoidal sigma weight residual 180.00 123.52 56.48 3 1.50e+01 4.44e-03 9.40e+00 dihedral pdb=" CA ASP A 389 " pdb=" CB ASP A 389 " pdb=" CG ASP A 389 " pdb=" OD1 ASP A 389 " ideal model delta sinusoidal sigma weight residual -30.00 -81.14 51.14 1 2.00e+01 2.50e-03 8.94e+00 dihedral pdb=" CB MET C 86 " pdb=" CG MET C 86 " pdb=" SD MET C 86 " pdb=" CE MET C 86 " ideal model delta sinusoidal sigma weight residual 180.00 129.24 50.76 3 1.50e+01 4.44e-03 8.94e+00 ... (remaining 2657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.424: 709 0.424 - 0.847: 0 0.847 - 1.271: 0 1.271 - 1.694: 0 1.694 - 2.118: 1 Chirality restraints: 710 Sorted by residual: chirality pdb=" C26 T69 D 1 " pdb=" C25 T69 D 1 " pdb=" N12 T69 D 1 " pdb=" S01 T69 D 1 " both_signs ideal model delta sigma weight residual False 3.12 1.00 2.12 2.00e-01 2.50e+01 1.12e+02 chirality pdb=" CA IML D 4 " pdb=" N IML D 4 " pdb=" C IML D 4 " pdb=" CB IML D 4 " both_signs ideal model delta sigma weight residual False 2.43 2.84 -0.40 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" CA MAA D 5 " pdb=" N MAA D 5 " pdb=" C MAA D 5 " pdb=" CB MAA D 5 " both_signs ideal model delta sigma weight residual False 2.48 2.78 -0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 707 not shown) Planarity restraints: 732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 439 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.91e+00 pdb=" C GLY A 439 " 0.038 2.00e-02 2.50e+03 pdb=" O GLY A 439 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA A 440 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 60 " -0.032 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO A 61 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 61 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 61 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 21 " -0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO A 22 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 22 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 22 " -0.024 5.00e-02 4.00e+02 ... (remaining 729 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.35: 14 2.35 - 2.91: 1830 2.91 - 3.47: 5353 3.47 - 4.04: 8575 4.04 - 4.60: 12554 Nonbonded interactions: 28326 Sorted by model distance: nonbonded pdb=" OD1 ASN A 300 " pdb=" HN1 0A1 D 2 " model vdw 1.783 2.450 nonbonded pdb=" HA IML D 4 " pdb=" HM3 MAA D 5 " model vdw 2.042 2.440 nonbonded pdb=" OD2 ASP A 139 " pdb=" OG SER A 141 " model vdw 2.177 2.800 nonbonded pdb=" O ILE A 68 " pdb=" HE2 0A1 D 2 " model vdw 2.177 2.450 nonbonded pdb=" HB1 MAA D 5 " pdb=" HM2 MAA D 5 " model vdw 2.201 2.440 ... (remaining 28321 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: 0.010 Normalize map: mean=0, sd=1: 0.840 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: 0.110 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.990 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 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 0.156 4431 Z= 0.347 Angle : 0.708 21.675 5997 Z= 0.370 Chirality : 0.091 2.118 710 Planarity : 0.005 0.049 732 Dihedral : 13.188 85.038 1621 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: 1.55 (0.35), residues: 543 helix: 1.69 (0.25), residues: 388 sheet: -1.32 (1.44), residues: 12 loop : -0.50 (0.51), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.002 0.000 HIS C 88 PHE 0.017 0.001 PHE A 217 TYR 0.007 0.001 TYR A 137 ARG 0.006 0.001 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.20065 ( 316) hydrogen bonds : angle 6.43995 ( 945) covalent geometry : bond 0.00622 ( 4429) covalent geometry : angle 0.70836 ( 5997) Misc. bond : bond 0.01311 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.459 Fit side-chains REVERT: B 31 LYS cc_start: 0.8113 (mppt) cc_final: 0.7711 (mppt) REVERT: A 27 GLN cc_start: 0.7407 (mm110) cc_final: 0.7001 (mm110) REVERT: A 117 LYS cc_start: 0.7491 (mttt) cc_final: 0.7201 (mtmm) REVERT: A 167 GLU cc_start: 0.7900 (tt0) cc_final: 0.7670 (tt0) REVERT: A 268 ARG cc_start: 0.6814 (ptp-110) cc_final: 0.6438 (ptm-80) REVERT: A 307 MET cc_start: 0.6089 (mmt) cc_final: 0.5278 (ttt) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 1.5257 time to fit residues: 113.2786 Evaluate side-chains 62 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.0870 chunk 27 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 0.0020 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 0.0050 overall best weight: 0.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.146359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.112546 restraints weight = 4729.506| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.87 r_work: 0.3353 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4431 Z= 0.103 Angle : 0.443 4.628 5997 Z= 0.233 Chirality : 0.036 0.132 710 Planarity : 0.004 0.033 732 Dihedral : 5.524 89.781 627 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.43 % Allowed : 6.90 % Favored : 92.67 % 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: 2.84 (0.36), residues: 543 helix: 2.66 (0.26), residues: 398 sheet: -0.71 (1.63), residues: 12 loop : -0.36 (0.52), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 90 HIS 0.003 0.001 HIS A 360 PHE 0.006 0.001 PHE A 112 TYR 0.007 0.001 TYR A 455 ARG 0.002 0.000 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.04227 ( 316) hydrogen bonds : angle 4.07580 ( 945) covalent geometry : bond 0.00199 ( 4429) covalent geometry : angle 0.44316 ( 5997) Misc. bond : bond 0.00084 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.498 Fit side-chains REVERT: A 27 GLN cc_start: 0.7756 (mm110) cc_final: 0.7487 (mm110) REVERT: A 268 ARG cc_start: 0.7540 (ptp-110) cc_final: 0.6839 (ptm-80) outliers start: 2 outliers final: 1 residues processed: 67 average time/residue: 1.2136 time to fit residues: 84.4901 Evaluate side-chains 61 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 0.0030 chunk 38 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 10 optimal weight: 0.0040 chunk 32 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN A 20 GLN A 241 ASN A 244 ASN A 275 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.145632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.111769 restraints weight = 4770.413| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.87 r_work: 0.3350 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4431 Z= 0.103 Angle : 0.402 4.560 5997 Z= 0.207 Chirality : 0.036 0.128 710 Planarity : 0.003 0.028 732 Dihedral : 5.230 86.649 627 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.86 % Allowed : 9.70 % Favored : 89.44 % 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: 3.28 (0.37), residues: 543 helix: 2.97 (0.26), residues: 401 sheet: -0.91 (1.54), residues: 12 loop : -0.16 (0.53), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 PHE 0.008 0.001 PHE B 49 TYR 0.009 0.001 TYR A 137 ARG 0.002 0.000 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.03806 ( 316) hydrogen bonds : angle 3.64744 ( 945) covalent geometry : bond 0.00214 ( 4429) covalent geometry : angle 0.40246 ( 5997) Misc. bond : bond 0.00040 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.450 Fit side-chains REVERT: A 15 ILE cc_start: 0.8014 (pt) cc_final: 0.7658 (mt) REVERT: A 27 GLN cc_start: 0.7652 (mm110) cc_final: 0.7398 (mm110) REVERT: A 139 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7893 (t70) REVERT: A 268 ARG cc_start: 0.7607 (ptp-110) cc_final: 0.7327 (ptm160) REVERT: A 405 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.6718 (mtt-85) outliers start: 4 outliers final: 0 residues processed: 65 average time/residue: 1.1967 time to fit residues: 80.8501 Evaluate side-chains 62 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 405 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN A 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.143650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.109232 restraints weight = 4760.595| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.88 r_work: 0.3314 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4431 Z= 0.134 Angle : 0.428 5.590 5997 Z= 0.220 Chirality : 0.037 0.132 710 Planarity : 0.003 0.027 732 Dihedral : 5.262 85.081 627 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.08 % Allowed : 10.99 % Favored : 87.93 % 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: 3.32 (0.37), residues: 543 helix: 2.95 (0.26), residues: 402 sheet: -0.79 (1.64), residues: 12 loop : -0.01 (0.54), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.003 0.001 HIS A 360 PHE 0.009 0.001 PHE B 49 TYR 0.010 0.001 TYR A 137 ARG 0.001 0.000 ARG A 236 Details of bonding type rmsd hydrogen bonds : bond 0.03920 ( 316) hydrogen bonds : angle 3.66442 ( 945) covalent geometry : bond 0.00296 ( 4429) covalent geometry : angle 0.42805 ( 5997) Misc. bond : bond 0.00015 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.527 Fit side-chains REVERT: A 15 ILE cc_start: 0.7982 (pt) cc_final: 0.7586 (mt) REVERT: A 20 GLN cc_start: 0.7666 (mt0) cc_final: 0.7421 (mt0) REVERT: A 27 GLN cc_start: 0.7463 (mm110) cc_final: 0.7202 (mm110) REVERT: A 139 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7842 (t70) REVERT: A 268 ARG cc_start: 0.7674 (ptp-110) cc_final: 0.7329 (ptm160) REVERT: A 273 ARG cc_start: 0.7920 (mtt180) cc_final: 0.6960 (mtp85) REVERT: A 405 ARG cc_start: 0.6955 (OUTLIER) cc_final: 0.6707 (mtt-85) outliers start: 5 outliers final: 2 residues processed: 65 average time/residue: 1.4165 time to fit residues: 95.2390 Evaluate side-chains 66 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 465 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 0.0980 chunk 44 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.144799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.110713 restraints weight = 4869.572| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.88 r_work: 0.3332 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4431 Z= 0.109 Angle : 0.400 4.453 5997 Z= 0.205 Chirality : 0.036 0.128 710 Planarity : 0.003 0.028 732 Dihedral : 5.173 84.673 627 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.65 % Allowed : 12.28 % Favored : 87.07 % 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: 3.55 (0.37), residues: 543 helix: 3.12 (0.26), residues: 402 sheet: -0.79 (1.68), residues: 12 loop : 0.04 (0.55), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 PHE 0.007 0.001 PHE A 261 TYR 0.007 0.001 TYR A 137 ARG 0.001 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 316) hydrogen bonds : angle 3.54493 ( 945) covalent geometry : bond 0.00233 ( 4429) covalent geometry : angle 0.39994 ( 5997) Misc. bond : bond 0.00009 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.509 Fit side-chains REVERT: A 15 ILE cc_start: 0.8017 (pt) cc_final: 0.7603 (mt) REVERT: A 20 GLN cc_start: 0.7676 (mt0) cc_final: 0.7405 (mt0) REVERT: A 27 GLN cc_start: 0.7486 (mm110) cc_final: 0.7267 (mm110) REVERT: A 139 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7807 (t70) REVERT: A 268 ARG cc_start: 0.7760 (ptp-110) cc_final: 0.7493 (ptm160) REVERT: A 273 ARG cc_start: 0.7975 (mtt180) cc_final: 0.6938 (mtp85) outliers start: 3 outliers final: 1 residues processed: 64 average time/residue: 1.3779 time to fit residues: 91.3261 Evaluate side-chains 63 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 465 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 36 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.143291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.108908 restraints weight = 4767.990| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.88 r_work: 0.3311 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4431 Z= 0.133 Angle : 0.424 5.361 5997 Z= 0.217 Chirality : 0.036 0.133 710 Planarity : 0.003 0.028 732 Dihedral : 5.222 84.155 627 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.29 % Allowed : 12.50 % Favored : 86.21 % 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: 3.49 (0.37), residues: 543 helix: 3.07 (0.26), residues: 402 sheet: -1.49 (1.51), residues: 14 loop : 0.19 (0.56), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 324 HIS 0.003 0.001 HIS A 360 PHE 0.009 0.001 PHE B 49 TYR 0.009 0.001 TYR A 137 ARG 0.001 0.000 ARG A 236 Details of bonding type rmsd hydrogen bonds : bond 0.03810 ( 316) hydrogen bonds : angle 3.59158 ( 945) covalent geometry : bond 0.00297 ( 4429) covalent geometry : angle 0.42364 ( 5997) Misc. bond : bond 0.00026 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.514 Fit side-chains REVERT: A 15 ILE cc_start: 0.8012 (pt) cc_final: 0.7599 (mt) REVERT: A 27 GLN cc_start: 0.7403 (mm110) cc_final: 0.7191 (mm110) REVERT: A 139 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7779 (t70) REVERT: A 268 ARG cc_start: 0.7740 (ptp-110) cc_final: 0.7421 (ptm160) REVERT: A 273 ARG cc_start: 0.8051 (mtt180) cc_final: 0.6984 (mtp85) outliers start: 6 outliers final: 3 residues processed: 61 average time/residue: 1.3628 time to fit residues: 86.0849 Evaluate side-chains 64 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 465 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 9 optimal weight: 0.0040 chunk 48 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN A 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.143985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.109689 restraints weight = 4747.737| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.88 r_work: 0.3322 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4431 Z= 0.115 Angle : 0.404 4.591 5997 Z= 0.207 Chirality : 0.036 0.129 710 Planarity : 0.003 0.028 732 Dihedral : 5.156 84.081 627 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.86 % Allowed : 13.15 % Favored : 85.99 % 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: 3.60 (0.37), residues: 543 helix: 3.15 (0.26), residues: 402 sheet: -1.04 (1.64), residues: 12 loop : 0.14 (0.55), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 PHE 0.007 0.001 PHE B 49 TYR 0.007 0.001 TYR A 137 ARG 0.001 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.03625 ( 316) hydrogen bonds : angle 3.52813 ( 945) covalent geometry : bond 0.00251 ( 4429) covalent geometry : angle 0.40425 ( 5997) Misc. bond : bond 0.00013 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.513 Fit side-chains REVERT: A 20 GLN cc_start: 0.7627 (mt0) cc_final: 0.7368 (mt0) REVERT: A 27 GLN cc_start: 0.7402 (mm110) cc_final: 0.7183 (mm110) REVERT: A 139 ASP cc_start: 0.8088 (OUTLIER) cc_final: 0.7768 (t70) REVERT: A 268 ARG cc_start: 0.7733 (ptp-110) cc_final: 0.7396 (ptm160) REVERT: A 273 ARG cc_start: 0.7996 (mtt180) cc_final: 0.6967 (mtp85) outliers start: 4 outliers final: 1 residues processed: 64 average time/residue: 1.3307 time to fit residues: 88.2671 Evaluate side-chains 63 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 230 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.1648 > 50: distance: 53 - 55: 8.836 distance: 55 - 56: 17.309 distance: 56 - 57: 16.195 distance: 57 - 58: 22.191 distance: 57 - 59: 22.170 distance: 60 - 61: 14.175 distance: 60 - 63: 16.760 distance: 61 - 62: 23.038 distance: 61 - 67: 10.913 distance: 62 - 97: 34.053 distance: 63 - 64: 19.912 distance: 64 - 65: 34.488 distance: 64 - 66: 25.238 distance: 67 - 68: 11.944 distance: 68 - 69: 10.906 distance: 68 - 71: 16.460 distance: 69 - 70: 13.889 distance: 69 - 73: 3.303 distance: 71 - 72: 22.599 distance: 73 - 74: 10.513 distance: 74 - 75: 13.513 distance: 74 - 77: 15.841 distance: 75 - 76: 26.511 distance: 75 - 85: 4.059 distance: 77 - 78: 5.510 distance: 78 - 79: 18.429 distance: 78 - 80: 16.094 distance: 79 - 81: 7.554 distance: 81 - 83: 17.251 distance: 82 - 83: 20.252 distance: 83 - 84: 18.345 distance: 85 - 86: 10.373 distance: 86 - 87: 7.467 distance: 86 - 89: 9.167 distance: 87 - 88: 12.652 distance: 87 - 97: 12.451 distance: 89 - 90: 8.948 distance: 90 - 91: 5.777 distance: 90 - 92: 4.062 distance: 91 - 93: 5.959 distance: 92 - 94: 3.638 distance: 93 - 95: 5.182 distance: 94 - 95: 5.452 distance: 95 - 96: 4.377 distance: 97 - 98: 6.958 distance: 98 - 99: 13.573 distance: 98 - 101: 17.373 distance: 99 - 100: 12.359 distance: 99 - 105: 26.940 distance: 101 - 102: 12.883 distance: 102 - 103: 14.653 distance: 102 - 104: 31.553 distance: 105 - 106: 12.772 distance: 106 - 107: 16.963 distance: 106 - 109: 16.661 distance: 107 - 108: 11.882 distance: 107 - 111: 7.835 distance: 109 - 110: 20.052 distance: 111 - 112: 4.653 distance: 111 - 117: 5.714 distance: 112 - 113: 13.177 distance: 112 - 115: 8.942 distance: 113 - 114: 18.479 distance: 113 - 118: 11.161 distance: 115 - 116: 9.295 distance: 116 - 117: 12.552 distance: 118 - 119: 19.791 distance: 118 - 124: 34.397 distance: 119 - 120: 5.855 distance: 119 - 122: 8.230 distance: 120 - 121: 10.314 distance: 120 - 125: 34.664 distance: 122 - 123: 38.371 distance: 123 - 124: 28.334 distance: 125 - 126: 22.536 distance: 126 - 127: 22.878 distance: 126 - 129: 14.572 distance: 127 - 128: 22.951 distance: 127 - 134: 11.443 distance: 129 - 130: 16.908 distance: 130 - 131: 11.826 distance: 131 - 132: 14.394 distance: 131 - 133: 10.740