Tue 25 Dec 19:27:55 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2gnr-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gnr-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gnr-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gnr-3.8-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gnr-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gnr-3.8-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Tue 25 Dec 19:28:05 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gnr-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gnr-3.8-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 201 and 0 Target number of residues in the AU: 201 Target solvent content: 0.6662 Checking the provided sequence file Detected sequence length: 145 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 290 Adjusted target solvent content: 0.52 Input MTZ file: 2gnr-3.8-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 91 Cell parameters: 75.160 75.160 115.370 90.000 90.000 90.000 Input sequence file: 2gnr-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 2320 target number of atoms Had to go as low as 0.70 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 75.160 3.801 Wilson plot Bfac: 88.62 3561 reflections ( 99.30 % complete ) and 0 restraints for refining 2587 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3415 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3388 (Rfree = 0.000) for 2587 atoms. Found 14 (14 requested) and removed 31 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.72 3.62 Search for helices and strands: 0 residues in 0 chains, 2626 seeds are put forward NCS extension: 0 residues added, 2626 seeds are put forward Round 1: 121 peptides, 24 chains. Longest chain 11 peptides. Score 0.310 Round 2: 136 peptides, 21 chains. Longest chain 15 peptides. Score 0.451 Round 3: 143 peptides, 23 chains. Longest chain 22 peptides. Score 0.442 Round 4: 157 peptides, 23 chains. Longest chain 16 peptides. Score 0.505 Round 5: 158 peptides, 21 chains. Longest chain 20 peptides. Score 0.547 Taking the results from Round 5 Chains 22, Residues 137, Estimated correctness of the model 0.0 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 3561 reflections ( 99.30 % complete ) and 4657 restraints for refining 2098 atoms. 4040 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2800 (Rfree = 0.000) for 2098 atoms. Found 7 (11 requested) and removed 19 (5 requested) atoms. Cycle 2: After refmac, R = 0.2538 (Rfree = 0.000) for 2051 atoms. Found 9 (11 requested) and removed 27 (5 requested) atoms. Cycle 3: After refmac, R = 0.2527 (Rfree = 0.000) for 2017 atoms. Found 5 (11 requested) and removed 12 (5 requested) atoms. Cycle 4: After refmac, R = 0.2097 (Rfree = 0.000) for 1998 atoms. Found 3 (11 requested) and removed 8 (5 requested) atoms. Cycle 5: After refmac, R = 0.2361 (Rfree = 0.000) for 1984 atoms. Found 4 (10 requested) and removed 13 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.67 3.57 Search for helices and strands: 0 residues in 0 chains, 2031 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 2061 seeds are put forward Round 1: 128 peptides, 23 chains. Longest chain 9 peptides. Score 0.369 Round 2: 165 peptides, 25 chains. Longest chain 14 peptides. Score 0.502 Round 3: 158 peptides, 22 chains. Longest chain 17 peptides. Score 0.528 Round 4: 178 peptides, 23 chains. Longest chain 18 peptides. Score 0.590 Round 5: 174 peptides, 24 chains. Longest chain 16 peptides. Score 0.557 Taking the results from Round 4 Chains 23, Residues 155, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3561 reflections ( 99.30 % complete ) and 4686 restraints for refining 2098 atoms. 4089 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2526 (Rfree = 0.000) for 2098 atoms. Found 2 (11 requested) and removed 20 (5 requested) atoms. Cycle 7: After refmac, R = 0.2434 (Rfree = 0.000) for 2070 atoms. Found 7 (11 requested) and removed 18 (5 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2484 (Rfree = 0.000) for 2049 atoms. Found 6 (11 requested) and removed 24 (5 requested) atoms. Cycle 9: After refmac, R = 0.2205 (Rfree = 0.000) for 2017 atoms. Found 2 (11 requested) and removed 14 (5 requested) atoms. Cycle 10: After refmac, R = 0.2052 (Rfree = 0.000) for 1999 atoms. Found 3 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.64 3.54 Search for helices and strands: 0 residues in 0 chains, 2071 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 2097 seeds are put forward Round 1: 130 peptides, 25 chains. Longest chain 10 peptides. Score 0.335 Round 2: 158 peptides, 26 chains. Longest chain 13 peptides. Score 0.452 Round 3: 150 peptides, 24 chains. Longest chain 15 peptides. Score 0.455 Round 4: 165 peptides, 25 chains. Longest chain 14 peptides. Score 0.502 Round 5: 155 peptides, 22 chains. Longest chain 15 peptides. Score 0.516 Taking the results from Round 5 Chains 22, Residues 133, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3561 reflections ( 99.30 % complete ) and 4876 restraints for refining 2098 atoms. 4366 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2409 (Rfree = 0.000) for 2098 atoms. Found 9 (11 requested) and removed 14 (5 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2685 (Rfree = 0.000) for 2079 atoms. Found 11 (11 requested) and removed 19 (5 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2650 (Rfree = 0.000) for 2044 atoms. Found 11 (11 requested) and removed 26 (5 requested) atoms. Cycle 14: After refmac, R = 0.2689 (Rfree = 0.000) for 2011 atoms. Found 11 (11 requested) and removed 40 (5 requested) atoms. Cycle 15: After refmac, R = 0.2709 (Rfree = 0.000) for 1972 atoms. Found 9 (10 requested) and removed 23 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.64 3.54 Search for helices and strands: 0 residues in 0 chains, 2038 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 2061 seeds are put forward Round 1: 112 peptides, 24 chains. Longest chain 7 peptides. Score 0.261 Round 2: 142 peptides, 23 chains. Longest chain 14 peptides. Score 0.438 Round 3: 135 peptides, 21 chains. Longest chain 15 peptides. Score 0.446 Round 4: 145 peptides, 20 chains. Longest chain 15 peptides. Score 0.511 Round 5: 139 peptides, 22 chains. Longest chain 14 peptides. Score 0.444 Taking the results from Round 4 Chains 20, Residues 125, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3561 reflections ( 99.30 % complete ) and 4558 restraints for refining 2026 atoms. 4078 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2641 (Rfree = 0.000) for 2026 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 17: After refmac, R = 0.2419 (Rfree = 0.000) for 2003 atoms. Found 7 (11 requested) and removed 11 (5 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2611 (Rfree = 0.000) for 1988 atoms. Found 10 (10 requested) and removed 37 (5 requested) atoms. Cycle 19: After refmac, R = 0.2200 (Rfree = 0.000) for 1951 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.1861 (Rfree = 0.000) for 1944 atoms. Found 4 (10 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.60 3.51 Search for helices and strands: 0 residues in 0 chains, 2005 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 2029 seeds are put forward Round 1: 126 peptides, 27 chains. Longest chain 9 peptides. Score 0.269 Round 2: 152 peptides, 27 chains. Longest chain 14 peptides. Score 0.403 Round 3: 142 peptides, 26 chains. Longest chain 8 peptides. Score 0.375 Round 4: 137 peptides, 21 chains. Longest chain 14 peptides. Score 0.455 Round 5: 127 peptides, 22 chains. Longest chain 9 peptides. Score 0.386 Taking the results from Round 4 Chains 21, Residues 116, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3561 reflections ( 99.30 % complete ) and 4656 restraints for refining 2064 atoms. 4213 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2686 (Rfree = 0.000) for 2064 atoms. Found 11 (11 requested) and removed 27 (5 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.2595 (Rfree = 0.000) for 2029 atoms. Found 7 (11 requested) and removed 25 (5 requested) atoms. Cycle 23: After refmac, R = 0.2424 (Rfree = 0.000) for 1995 atoms. Found 11 (11 requested) and removed 29 (5 requested) atoms. Cycle 24: After refmac, R = 0.2160 (Rfree = 0.000) for 1964 atoms. Found 9 (10 requested) and removed 24 (5 requested) atoms. Cycle 25: After refmac, R = 0.2215 (Rfree = 0.000) for 1942 atoms. Found 10 (10 requested) and removed 18 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.59 3.50 Search for helices and strands: 0 residues in 0 chains, 2006 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2020 seeds are put forward Round 1: 110 peptides, 24 chains. Longest chain 7 peptides. Score 0.249 Round 2: 133 peptides, 25 chains. Longest chain 10 peptides. Score 0.351 Round 3: 133 peptides, 21 chains. Longest chain 10 peptides. Score 0.436 Round 4: 136 peptides, 22 chains. Longest chain 12 peptides. Score 0.430 Round 5: 136 peptides, 24 chains. Longest chain 10 peptides. Score 0.388 Taking the results from Round 3 Chains 21, Residues 112, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3561 reflections ( 99.30 % complete ) and 4210 restraints for refining 1975 atoms. 3758 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2386 (Rfree = 0.000) for 1975 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 27: After refmac, R = 0.2316 (Rfree = 0.000) for 1957 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 28: After refmac, R = 0.2267 (Rfree = 0.000) for 1946 atoms. Found 9 (10 requested) and removed 11 (5 requested) atoms. Cycle 29: After refmac, R = 0.2155 (Rfree = 0.000) for 1936 atoms. Found 8 (10 requested) and removed 13 (5 requested) atoms. Cycle 30: After refmac, R = 0.2148 (Rfree = 0.000) for 1921 atoms. Found 5 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.64 3.54 Search for helices and strands: 0 residues in 0 chains, 1996 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 2005 seeds are put forward Round 1: 109 peptides, 23 chains. Longest chain 8 peptides. Score 0.267 Round 2: 131 peptides, 23 chains. Longest chain 11 peptides. Score 0.384 Round 3: 118 peptides, 20 chains. Longest chain 10 peptides. Score 0.384 Round 4: 136 peptides, 22 chains. Longest chain 9 peptides. Score 0.430 Round 5: 135 peptides, 20 chains. Longest chain 12 peptides. Score 0.466 Taking the results from Round 5 Chains 20, Residues 115, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3561 reflections ( 99.30 % complete ) and 4519 restraints for refining 2052 atoms. 4079 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2526 (Rfree = 0.000) for 2052 atoms. Found 11 (11 requested) and removed 20 (5 requested) atoms. Cycle 32: After refmac, R = 0.2321 (Rfree = 0.000) for 2029 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2209 (Rfree = 0.000) for 2021 atoms. Found 11 (11 requested) and removed 30 (5 requested) atoms. Cycle 34: After refmac, R = 0.2282 (Rfree = 0.000) for 1996 atoms. Found 10 (10 requested) and removed 22 (5 requested) atoms. Cycle 35: After refmac, R = 0.2394 (Rfree = 0.000) for 1978 atoms. Found 10 (10 requested) and removed 25 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.67 3.57 Search for helices and strands: 0 residues in 0 chains, 2022 seeds are put forward NCS extension: 0 residues added, 2022 seeds are put forward Round 1: 93 peptides, 21 chains. Longest chain 7 peptides. Score 0.222 Round 2: 109 peptides, 23 chains. Longest chain 6 peptides. Score 0.267 Round 3: 103 peptides, 18 chains. Longest chain 11 peptides. Score 0.351 Round 4: 107 peptides, 18 chains. Longest chain 12 peptides. Score 0.373 Round 5: 107 peptides, 19 chains. Longest chain 11 peptides. Score 0.349 Taking the results from Round 4 Chains 18, Residues 89, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3561 reflections ( 99.30 % complete ) and 4694 restraints for refining 2071 atoms. 4339 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2509 (Rfree = 0.000) for 2071 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2307 (Rfree = 0.000) for 2061 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 38: After refmac, R = 0.2470 (Rfree = 0.000) for 2045 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 39: After refmac, R = 0.2261 (Rfree = 0.000) for 2035 atoms. Found 10 (11 requested) and removed 10 (5 requested) atoms. Cycle 40: After refmac, R = 0.2140 (Rfree = 0.000) for 2031 atoms. Found 10 (11 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.67 3.57 Search for helices and strands: 0 residues in 0 chains, 2072 seeds are put forward NCS extension: 0 residues added, 2072 seeds are put forward Round 1: 85 peptides, 20 chains. Longest chain 6 peptides. Score 0.198 Round 2: 99 peptides, 21 chains. Longest chain 7 peptides. Score 0.258 Round 3: 102 peptides, 18 chains. Longest chain 10 peptides. Score 0.346 Round 4: 104 peptides, 20 chains. Longest chain 9 peptides. Score 0.310 Round 5: 107 peptides, 20 chains. Longest chain 9 peptides. Score 0.326 Taking the results from Round 3 Chains 18, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3561 reflections ( 99.30 % complete ) and 4678 restraints for refining 2020 atoms. 4360 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2227 (Rfree = 0.000) for 2020 atoms. Found 8 (11 requested) and removed 15 (5 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2248 (Rfree = 0.000) for 2001 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 43: After refmac, R = 0.2366 (Rfree = 0.000) for 1995 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 44: After refmac, R = 0.2339 (Rfree = 0.000) for 1989 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.2274 (Rfree = 0.000) for 1978 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.72 3.62 Search for helices and strands: 0 residues in 0 chains, 2043 seeds are put forward NCS extension: 0 residues added, 2043 seeds are put forward Round 1: 74 peptides, 16 chains. Longest chain 8 peptides. Score 0.233 Round 2: 78 peptides, 16 chains. Longest chain 8 peptides. Score 0.258 Round 3: 71 peptides, 14 chains. Longest chain 8 peptides. Score 0.268 Round 4: 77 peptides, 15 chains. Longest chain 8 peptides. Score 0.278 Round 5: 73 peptides, 15 chains. Longest chain 10 peptides. Score 0.253 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2gnr-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3561 reflections ( 99.30 % complete ) and 4474 restraints for refining 1915 atoms. 4241 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2114 (Rfree = 0.000) for 1915 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2262 (Rfree = 0.000) for 1906 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.2151 (Rfree = 0.000) for 1897 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2433 (Rfree = 0.000) for 1889 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Writing output files ... Failed to save intermediate PDBFailed to save intermediate PDB Normal termination of warpNtrace Tue 25 Dec 20:10:56 GMT 2018 Job finished. Failed to save intermediate PDB TimeTaking 43.02