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 2ooj-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ooj-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ooj-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ooj-3.4-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/2ooj-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ooj-3.4-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/2ooj-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ooj-3.4-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 193 and 0 Target number of residues in the AU: 193 Target solvent content: 0.6226 Checking the provided sequence file Detected sequence length: 141 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 282 Adjusted target solvent content: 0.45 Input MTZ file: 2ooj-3.4-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: 19 Cell parameters: 47.211 55.254 106.086 90.000 90.000 90.000 Input sequence file: 2ooj-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 2256 target number of atoms Had to go as low as 0.60 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: 53.043 3.400 Wilson plot Bfac: 61.81 4089 reflections ( 99.18 % complete ) and 0 restraints for refining 2491 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3498 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3091 (Rfree = 0.000) for 2491 atoms. Found 18 (18 requested) and removed 23 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.25 3.47 Search for helices and strands: 0 residues in 0 chains, 2512 seeds are put forward NCS extension: 0 residues added, 2512 seeds are put forward Round 1: 92 peptides, 19 chains. Longest chain 9 peptides. Score 0.278 Round 2: 105 peptides, 17 chains. Longest chain 12 peptides. Score 0.412 Round 3: 109 peptides, 17 chains. Longest chain 11 peptides. Score 0.435 Round 4: 125 peptides, 19 chains. Longest chain 14 peptides. Score 0.475 Round 5: 128 peptides, 19 chains. Longest chain 12 peptides. Score 0.490 Taking the results from Round 5 Chains 19, Residues 109, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4089 reflections ( 99.18 % complete ) and 4793 restraints for refining 2052 atoms. 4376 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2423 (Rfree = 0.000) for 2052 atoms. Found 8 (15 requested) and removed 13 (7 requested) atoms. Cycle 2: After refmac, R = 0.2408 (Rfree = 0.000) for 2023 atoms. Found 11 (15 requested) and removed 8 (7 requested) atoms. Cycle 3: After refmac, R = 0.2301 (Rfree = 0.000) for 2019 atoms. Found 9 (15 requested) and removed 10 (7 requested) atoms. Cycle 4: After refmac, R = 0.2409 (Rfree = 0.000) for 2007 atoms. Found 4 (15 requested) and removed 10 (7 requested) atoms. Cycle 5: After refmac, R = 0.2230 (Rfree = 0.000) for 1996 atoms. Found 6 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.28 3.51 Search for helices and strands: 0 residues in 0 chains, 2042 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 2055 seeds are put forward Round 1: 106 peptides, 21 chains. Longest chain 10 peptides. Score 0.314 Round 2: 121 peptides, 18 chains. Longest chain 11 peptides. Score 0.477 Round 3: 128 peptides, 18 chains. Longest chain 17 peptides. Score 0.513 Round 4: 129 peptides, 18 chains. Longest chain 13 peptides. Score 0.518 Round 5: 134 peptides, 19 chains. Longest chain 14 peptides. Score 0.521 Taking the results from Round 5 Chains 20, Residues 115, Estimated correctness of the model 0.8 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4089 reflections ( 99.18 % complete ) and 4716 restraints for refining 2052 atoms. 4238 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2426 (Rfree = 0.000) for 2052 atoms. Found 8 (15 requested) and removed 15 (7 requested) atoms. Cycle 7: After refmac, R = 0.2456 (Rfree = 0.000) for 2031 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2343 (Rfree = 0.000) for 2029 atoms. Found 5 (15 requested) and removed 10 (7 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2351 (Rfree = 0.000) for 2023 atoms. Found 10 (15 requested) and removed 9 (7 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2485 (Rfree = 0.000) for 2019 atoms. Found 8 (15 requested) and removed 19 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.23 3.45 Search for helices and strands: 0 residues in 0 chains, 2044 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2059 seeds are put forward Round 1: 114 peptides, 21 chains. Longest chain 13 peptides. Score 0.363 Round 2: 139 peptides, 21 chains. Longest chain 14 peptides. Score 0.502 Round 3: 147 peptides, 20 chains. Longest chain 16 peptides. Score 0.562 Round 4: 122 peptides, 17 chains. Longest chain 13 peptides. Score 0.505 Round 5: 130 peptides, 17 chains. Longest chain 14 peptides. Score 0.545 Taking the results from Round 3 Chains 20, Residues 127, Estimated correctness of the model 15.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4089 reflections ( 99.18 % complete ) and 4770 restraints for refining 2052 atoms. 4282 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2470 (Rfree = 0.000) for 2052 atoms. Found 8 (15 requested) and removed 9 (7 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2579 (Rfree = 0.000) for 2042 atoms. Found 12 (15 requested) and removed 15 (7 requested) atoms. Cycle 13: After refmac, R = 0.2484 (Rfree = 0.000) for 2037 atoms. Found 8 (15 requested) and removed 9 (7 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2507 (Rfree = 0.000) for 2035 atoms. Found 5 (15 requested) and removed 11 (7 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.2457 (Rfree = 0.000) for 2028 atoms. Found 1 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.25 3.47 Search for helices and strands: 0 residues in 0 chains, 2068 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 2080 seeds are put forward Round 1: 106 peptides, 20 chains. Longest chain 12 peptides. Score 0.341 Round 2: 113 peptides, 15 chains. Longest chain 15 peptides. Score 0.505 Round 3: 127 peptides, 20 chains. Longest chain 12 peptides. Score 0.462 Round 4: 127 peptides, 17 chains. Longest chain 13 peptides. Score 0.530 Round 5: 127 peptides, 19 chains. Longest chain 13 peptides. Score 0.485 Taking the results from Round 4 Chains 17, Residues 110, Estimated correctness of the model 4.2 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4089 reflections ( 99.18 % complete ) and 4717 restraints for refining 2051 atoms. 4267 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2394 (Rfree = 0.000) for 2051 atoms. Found 11 (15 requested) and removed 15 (7 requested) atoms. Cycle 17: After refmac, R = 0.2233 (Rfree = 0.000) for 2041 atoms. Found 5 (15 requested) and removed 9 (7 requested) atoms. Cycle 18: After refmac, R = 0.2205 (Rfree = 0.000) for 2037 atoms. Found 2 (15 requested) and removed 7 (7 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2181 (Rfree = 0.000) for 2032 atoms. Found 3 (15 requested) and removed 7 (7 requested) atoms. Cycle 20: After refmac, R = 0.2184 (Rfree = 0.000) for 2026 atoms. Found 2 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.27 3.50 Search for helices and strands: 0 residues in 0 chains, 2058 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 2071 seeds are put forward Round 1: 109 peptides, 20 chains. Longest chain 11 peptides. Score 0.359 Round 2: 116 peptides, 16 chains. Longest chain 19 peptides. Score 0.497 Round 3: 122 peptides, 19 chains. Longest chain 14 peptides. Score 0.458 Round 4: 121 peptides, 19 chains. Longest chain 14 peptides. Score 0.453 Round 5: 118 peptides, 18 chains. Longest chain 18 peptides. Score 0.461 Taking the results from Round 2 Chains 16, Residues 100, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4089 reflections ( 99.18 % complete ) and 4836 restraints for refining 2021 atoms. 4452 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2275 (Rfree = 0.000) for 2021 atoms. Found 8 (15 requested) and removed 9 (7 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.2316 (Rfree = 0.000) for 2016 atoms. Found 5 (15 requested) and removed 12 (7 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2549 (Rfree = 0.000) for 2007 atoms. Found 11 (15 requested) and removed 12 (7 requested) atoms. Cycle 24: After refmac, R = 0.2346 (Rfree = 0.000) for 2005 atoms. Found 5 (15 requested) and removed 8 (7 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.2129 (Rfree = 0.000) for 2002 atoms. Found 3 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.30 3.53 Search for helices and strands: 0 residues in 0 chains, 2042 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 2062 seeds are put forward Round 1: 110 peptides, 24 chains. Longest chain 8 peptides. Score 0.260 Round 2: 121 peptides, 20 chains. Longest chain 11 peptides. Score 0.429 Round 3: 126 peptides, 19 chains. Longest chain 12 peptides. Score 0.480 Round 4: 142 peptides, 21 chains. Longest chain 21 peptides. Score 0.517 Round 5: 142 peptides, 22 chains. Longest chain 12 peptides. Score 0.495 Taking the results from Round 4 Chains 21, Residues 121, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4089 reflections ( 99.18 % complete ) and 4725 restraints for refining 2052 atoms. 4262 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2382 (Rfree = 0.000) for 2052 atoms. Found 4 (15 requested) and removed 12 (7 requested) atoms. Cycle 27: After refmac, R = 0.2389 (Rfree = 0.000) for 2038 atoms. Found 6 (15 requested) and removed 9 (7 requested) atoms. Cycle 28: After refmac, R = 0.2429 (Rfree = 0.000) for 2035 atoms. Found 3 (15 requested) and removed 8 (7 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2421 (Rfree = 0.000) for 2028 atoms. Found 4 (15 requested) and removed 7 (7 requested) atoms. Cycle 30: After refmac, R = 0.2471 (Rfree = 0.000) for 2025 atoms. Found 2 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.21 3.43 Search for helices and strands: 0 residues in 0 chains, 2062 seeds are put forward NCS extension: 33 residues added (3 deleted due to clashes), 2095 seeds are put forward Round 1: 103 peptides, 21 chains. Longest chain 10 peptides. Score 0.295 Round 2: 108 peptides, 17 chains. Longest chain 12 peptides. Score 0.429 Round 3: 120 peptides, 17 chains. Longest chain 17 peptides. Score 0.495 Round 4: 115 peptides, 19 chains. Longest chain 10 peptides. Score 0.420 Round 5: 108 peptides, 17 chains. Longest chain 10 peptides. Score 0.429 Taking the results from Round 3 Chains 17, Residues 103, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4089 reflections ( 99.18 % complete ) and 4862 restraints for refining 2052 atoms. 4437 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2459 (Rfree = 0.000) for 2052 atoms. Found 9 (15 requested) and removed 52 (7 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2369 (Rfree = 0.000) for 2006 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 33: After refmac, R = 0.2300 (Rfree = 0.000) for 2011 atoms. Found 5 (15 requested) and removed 8 (7 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.2244 (Rfree = 0.000) for 2007 atoms. Found 3 (15 requested) and removed 7 (7 requested) atoms. Cycle 35: After refmac, R = 0.2244 (Rfree = 0.000) for 2003 atoms. Found 1 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.26 3.49 Search for helices and strands: 0 residues in 0 chains, 2027 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2043 seeds are put forward Round 1: 90 peptides, 16 chains. Longest chain 11 peptides. Score 0.348 Round 2: 100 peptides, 18 chains. Longest chain 8 peptides. Score 0.356 Round 3: 105 peptides, 15 chains. Longest chain 14 peptides. Score 0.462 Round 4: 112 peptides, 19 chains. Longest chain 11 peptides. Score 0.402 Round 5: 111 peptides, 17 chains. Longest chain 14 peptides. Score 0.446 Taking the results from Round 3 Chains 16, Residues 90, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4089 reflections ( 99.18 % complete ) and 4867 restraints for refining 2042 atoms. 4489 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2200 (Rfree = 0.000) for 2042 atoms. Found 7 (15 requested) and removed 11 (7 requested) atoms. Cycle 37: After refmac, R = 0.2114 (Rfree = 0.000) for 2034 atoms. Found 4 (15 requested) and removed 7 (7 requested) atoms. Cycle 38: After refmac, R = 0.2087 (Rfree = 0.000) for 2030 atoms. Found 1 (15 requested) and removed 7 (7 requested) atoms. Cycle 39: After refmac, R = 0.2096 (Rfree = 0.000) for 2024 atoms. Found 3 (15 requested) and removed 7 (7 requested) atoms. Cycle 40: After refmac, R = 0.2133 (Rfree = 0.000) for 2019 atoms. Found 1 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.28 3.51 Search for helices and strands: 0 residues in 0 chains, 2056 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 2077 seeds are put forward Round 1: 89 peptides, 19 chains. Longest chain 7 peptides. Score 0.258 Round 2: 106 peptides, 17 chains. Longest chain 12 peptides. Score 0.418 Round 3: 109 peptides, 16 chains. Longest chain 14 peptides. Score 0.460 Round 4: 104 peptides, 15 chains. Longest chain 14 peptides. Score 0.457 Round 5: 99 peptides, 16 chains. Longest chain 13 peptides. Score 0.403 Taking the results from Round 3 Chains 16, Residues 93, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4089 reflections ( 99.18 % complete ) and 5101 restraints for refining 2052 atoms. 4745 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2445 (Rfree = 0.000) for 2052 atoms. Found 12 (15 requested) and removed 10 (7 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2304 (Rfree = 0.000) for 2046 atoms. Found 8 (15 requested) and removed 8 (7 requested) atoms. Cycle 43: After refmac, R = 0.2070 (Rfree = 0.000) for 2043 atoms. Found 1 (15 requested) and removed 7 (7 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.2034 (Rfree = 0.000) for 2036 atoms. Found 2 (15 requested) and removed 8 (7 requested) atoms. Cycle 45: After refmac, R = 0.2128 (Rfree = 0.000) for 2028 atoms. Found 8 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.28 3.51 Search for helices and strands: 0 residues in 0 chains, 2066 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 2080 seeds are put forward Round 1: 86 peptides, 17 chains. Longest chain 9 peptides. Score 0.294 Round 2: 106 peptides, 19 chains. Longest chain 11 peptides. Score 0.367 Round 3: 96 peptides, 17 chains. Longest chain 13 peptides. Score 0.358 Round 4: 111 peptides, 18 chains. Longest chain 14 peptides. Score 0.422 Round 5: 112 peptides, 17 chains. Longest chain 14 peptides. Score 0.452 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 95, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence Sequence coverage is 14 % Consider running further cycles of model building using 2ooj-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 95 A and 105 A 16 chains (102 residues) following loop building 1 chains (23 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4089 reflections ( 99.18 % complete ) and 4708 restraints for refining 2052 atoms. 4236 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2309 (Rfree = 0.000) for 2052 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2175 (Rfree = 0.000) for 2040 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2151 (Rfree = 0.000) for 2030 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.2149 (Rfree = 0.000) for 2019 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:11:22 GMT 2018 Job finished. TimeTaking 43.46