Sun 23 Dec 22:22:44 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 2gpj-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gpj-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gpj-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gpj-3.6-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/2gpj-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gpj-3.6-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 ============================================================ Sun 23 Dec 22:22:53 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/2gpj-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gpj-3.6-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 221 and 0 Target number of residues in the AU: 221 Target solvent content: 0.6495 Checking the provided sequence file Detected sequence length: 252 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 252 Adjusted target solvent content: 0.60 Input MTZ file: 2gpj-3.6-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: 92 Cell parameters: 100.540 100.540 67.510 90.000 90.000 90.000 Input sequence file: 2gpj-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 2016 target number of atoms Had to go as low as 0.75 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 Loops will be built when appropriate and at the last cycle Resolution range: 71.093 3.600 Wilson plot Bfac: 77.64 4295 reflections ( 99.44 % complete ) and 0 restraints for refining 2254 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3810 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3603 (Rfree = 0.000) for 2254 atoms. Found 14 (14 requested) and removed 23 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.50 3.06 Search for helices and strands: 0 residues in 0 chains, 2268 seeds are put forward Round 1: 81 peptides, 17 chains. Longest chain 7 peptides. Score 0.248 Round 2: 110 peptides, 23 chains. Longest chain 8 peptides. Score 0.269 Round 3: 119 peptides, 21 chains. Longest chain 13 peptides. Score 0.361 Round 4: 129 peptides, 20 chains. Longest chain 15 peptides. Score 0.430 Round 5: 118 peptides, 17 chains. Longest chain 15 peptides. Score 0.441 Taking the results from Round 5 Chains 17, Residues 101, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4295 reflections ( 99.44 % complete ) and 4304 restraints for refining 1827 atoms. 3917 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2781 (Rfree = 0.000) for 1827 atoms. Found 4 (11 requested) and removed 35 (5 requested) atoms. Cycle 2: After refmac, R = 0.2685 (Rfree = 0.000) for 1780 atoms. Found 4 (11 requested) and removed 33 (5 requested) atoms. Cycle 3: After refmac, R = 0.2781 (Rfree = 0.000) for 1747 atoms. Found 5 (11 requested) and removed 20 (5 requested) atoms. Cycle 4: After refmac, R = 0.2607 (Rfree = 0.000) for 1725 atoms. Found 6 (11 requested) and removed 21 (5 requested) atoms. Cycle 5: After refmac, R = 0.2535 (Rfree = 0.000) for 1705 atoms. Found 5 (10 requested) and removed 13 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.54 3.09 Search for helices and strands: 0 residues in 0 chains, 1751 seeds are put forward Round 1: 119 peptides, 23 chains. Longest chain 13 peptides. Score 0.317 Round 2: 137 peptides, 25 chains. Longest chain 16 peptides. Score 0.365 Round 3: 140 peptides, 25 chains. Longest chain 14 peptides. Score 0.379 Round 4: 139 peptides, 24 chains. Longest chain 14 peptides. Score 0.395 Round 5: 133 peptides, 21 chains. Longest chain 18 peptides. Score 0.428 Taking the results from Round 5 Chains 22, Residues 112, Estimated correctness of the model 0.0 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 4295 reflections ( 99.44 % complete ) and 3839 restraints for refining 1827 atoms. 3341 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2734 (Rfree = 0.000) for 1827 atoms. Found 5 (11 requested) and removed 14 (5 requested) atoms. Cycle 7: After refmac, R = 0.2679 (Rfree = 0.000) for 1801 atoms. Found 10 (11 requested) and removed 18 (5 requested) atoms. Cycle 8: After refmac, R = 0.2644 (Rfree = 0.000) for 1786 atoms. Found 7 (11 requested) and removed 13 (5 requested) atoms. Cycle 9: After refmac, R = 0.2488 (Rfree = 0.000) for 1774 atoms. Found 6 (11 requested) and removed 20 (5 requested) atoms. Cycle 10: After refmac, R = 0.2272 (Rfree = 0.000) for 1758 atoms. Found 2 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.54 3.09 Search for helices and strands: 0 residues in 0 chains, 1808 seeds are put forward Round 1: 130 peptides, 25 chains. Longest chain 12 peptides. Score 0.330 Round 2: 135 peptides, 21 chains. Longest chain 12 peptides. Score 0.437 Round 3: 142 peptides, 24 chains. Longest chain 11 peptides. Score 0.409 Round 4: 134 peptides, 21 chains. Longest chain 14 peptides. Score 0.432 Round 5: 135 peptides, 22 chains. Longest chain 13 peptides. Score 0.417 Taking the results from Round 2 Chains 21, Residues 114, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 4295 reflections ( 99.44 % complete ) and 4063 restraints for refining 1827 atoms. 3598 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3051 (Rfree = 0.000) for 1827 atoms. Found 11 (11 requested) and removed 24 (5 requested) atoms. Cycle 12: After refmac, R = 0.2836 (Rfree = 0.000) for 1804 atoms. Found 11 (11 requested) and removed 23 (5 requested) atoms. Cycle 13: After refmac, R = 0.2749 (Rfree = 0.000) for 1781 atoms. Found 9 (11 requested) and removed 9 (5 requested) atoms. Cycle 14: After refmac, R = 0.2490 (Rfree = 0.000) for 1779 atoms. Found 4 (11 requested) and removed 8 (5 requested) atoms. Cycle 15: After refmac, R = 0.2624 (Rfree = 0.000) for 1775 atoms. Found 2 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.61 3.15 Search for helices and strands: 0 residues in 0 chains, 1805 seeds are put forward Round 1: 125 peptides, 26 chains. Longest chain 8 peptides. Score 0.282 Round 2: 131 peptides, 23 chains. Longest chain 10 peptides. Score 0.377 Round 3: 135 peptides, 22 chains. Longest chain 16 peptides. Score 0.417 Round 4: 140 peptides, 22 chains. Longest chain 12 peptides. Score 0.440 Round 5: 148 peptides, 24 chains. Longest chain 14 peptides. Score 0.436 Taking the results from Round 4 Chains 22, Residues 118, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4295 reflections ( 99.44 % complete ) and 4079 restraints for refining 1827 atoms. 3629 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2893 (Rfree = 0.000) for 1827 atoms. Found 10 (11 requested) and removed 10 (5 requested) atoms. Cycle 17: After refmac, R = 0.2880 (Rfree = 0.000) for 1814 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 18: After refmac, R = 0.2793 (Rfree = 0.000) for 1815 atoms. Found 7 (11 requested) and removed 15 (5 requested) atoms. Cycle 19: After refmac, R = 0.2711 (Rfree = 0.000) for 1804 atoms. Found 4 (11 requested) and removed 8 (5 requested) atoms. Cycle 20: After refmac, R = 0.2689 (Rfree = 0.000) for 1792 atoms. Found 4 (11 requested) and removed 13 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.54 3.09 Search for helices and strands: 0 residues in 0 chains, 1816 seeds are put forward Round 1: 101 peptides, 22 chains. Longest chain 7 peptides. Score 0.243 Round 2: 116 peptides, 20 chains. Longest chain 10 peptides. Score 0.367 Round 3: 124 peptides, 19 chains. Longest chain 11 peptides. Score 0.427 Round 4: 129 peptides, 20 chains. Longest chain 13 peptides. Score 0.430 Round 5: 127 peptides, 21 chains. Longest chain 14 peptides. Score 0.400 Taking the results from Round 4 Chains 20, Residues 109, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4295 reflections ( 99.44 % complete ) and 4080 restraints for refining 1827 atoms. 3641 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2609 (Rfree = 0.000) for 1827 atoms. Found 4 (11 requested) and removed 5 (5 requested) atoms. Cycle 22: After refmac, R = 0.2473 (Rfree = 0.000) for 1818 atoms. Found 2 (11 requested) and removed 9 (5 requested) atoms. Cycle 23: After refmac, R = 0.2430 (Rfree = 0.000) for 1805 atoms. Found 1 (11 requested) and removed 9 (5 requested) atoms. Cycle 24: After refmac, R = 0.2403 (Rfree = 0.000) for 1794 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.2487 (Rfree = 0.000) for 1789 atoms. Found 5 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.54 3.09 Search for helices and strands: 0 residues in 0 chains, 1813 seeds are put forward Round 1: 96 peptides, 19 chains. Longest chain 9 peptides. Score 0.285 Round 2: 113 peptides, 19 chains. Longest chain 14 peptides. Score 0.374 Round 3: 121 peptides, 19 chains. Longest chain 13 peptides. Score 0.413 Round 4: 121 peptides, 19 chains. Longest chain 12 peptides. Score 0.413 Round 5: 126 peptides, 20 chains. Longest chain 13 peptides. Score 0.416 Taking the results from Round 5 Chains 20, Residues 106, Estimated correctness of the model 0.0 % 3 chains (11 residues) have been docked in sequence ------------------------------------------------------ 4295 reflections ( 99.44 % complete ) and 4040 restraints for refining 1827 atoms. 3621 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2681 (Rfree = 0.000) for 1827 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 27: After refmac, R = 0.2525 (Rfree = 0.000) for 1817 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 28: After refmac, R = 0.2500 (Rfree = 0.000) for 1812 atoms. Found 5 (11 requested) and removed 6 (5 requested) atoms. Cycle 29: After refmac, R = 0.2489 (Rfree = 0.000) for 1810 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. Cycle 30: After refmac, R = 0.2480 (Rfree = 0.000) for 1805 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.57 3.12 Search for helices and strands: 0 residues in 0 chains, 1815 seeds are put forward Round 1: 111 peptides, 21 chains. Longest chain 12 peptides. Score 0.320 Round 2: 113 peptides, 21 chains. Longest chain 12 peptides. Score 0.330 Round 3: 125 peptides, 19 chains. Longest chain 15 peptides. Score 0.432 Round 4: 121 peptides, 21 chains. Longest chain 13 peptides. Score 0.370 Round 5: 125 peptides, 20 chains. Longest chain 14 peptides. Score 0.411 Taking the results from Round 3 Chains 19, Residues 106, Estimated correctness of the model 0.0 % 6 chains (39 residues) have been docked in sequence ------------------------------------------------------ 4295 reflections ( 99.44 % complete ) and 3694 restraints for refining 1827 atoms. 3174 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2726 (Rfree = 0.000) for 1827 atoms. Found 9 (11 requested) and removed 14 (5 requested) atoms. Cycle 32: After refmac, R = 0.2530 (Rfree = 0.000) for 1810 atoms. Found 4 (11 requested) and removed 8 (5 requested) atoms. Cycle 33: After refmac, R = 0.2458 (Rfree = 0.000) for 1801 atoms. Found 5 (11 requested) and removed 5 (5 requested) atoms. Cycle 34: After refmac, R = 0.2417 (Rfree = 0.000) for 1799 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. Cycle 35: After refmac, R = 0.2410 (Rfree = 0.000) for 1792 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.55 3.10 Search for helices and strands: 0 residues in 0 chains, 1817 seeds are put forward Round 1: 100 peptides, 21 chains. Longest chain 8 peptides. Score 0.260 Round 2: 114 peptides, 20 chains. Longest chain 13 peptides. Score 0.357 Round 3: 114 peptides, 20 chains. Longest chain 10 peptides. Score 0.357 Round 4: 112 peptides, 18 chains. Longest chain 13 peptides. Score 0.391 Round 5: 105 peptides, 17 chains. Longest chain 15 peptides. Score 0.378 Taking the results from Round 4 Chains 18, Residues 94, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4295 reflections ( 99.44 % complete ) and 4174 restraints for refining 1827 atoms. 3816 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2497 (Rfree = 0.000) for 1827 atoms. Found 5 (11 requested) and removed 6 (5 requested) atoms. Cycle 37: After refmac, R = 0.2476 (Rfree = 0.000) for 1821 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. Cycle 38: After refmac, R = 0.2202 (Rfree = 0.000) for 1811 atoms. Found 3 (11 requested) and removed 8 (5 requested) atoms. Cycle 39: After refmac, R = 0.2185 (Rfree = 0.000) for 1804 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. Cycle 40: After refmac, R = 0.2174 (Rfree = 0.000) for 1800 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.54 3.09 Search for helices and strands: 0 residues in 0 chains, 1814 seeds are put forward Round 1: 105 peptides, 19 chains. Longest chain 14 peptides. Score 0.333 Round 2: 109 peptides, 19 chains. Longest chain 9 peptides. Score 0.354 Round 3: 110 peptides, 17 chains. Longest chain 15 peptides. Score 0.403 Round 4: 107 peptides, 18 chains. Longest chain 12 peptides. Score 0.366 Round 5: 102 peptides, 16 chains. Longest chain 15 peptides. Score 0.386 Taking the results from Round 3 Chains 17, Residues 93, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4295 reflections ( 99.44 % complete ) and 4137 restraints for refining 1827 atoms. 3768 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2467 (Rfree = 0.000) for 1827 atoms. Found 5 (11 requested) and removed 9 (5 requested) atoms. Cycle 42: After refmac, R = 0.2384 (Rfree = 0.000) for 1820 atoms. Found 2 (11 requested) and removed 7 (5 requested) atoms. Cycle 43: After refmac, R = 0.2348 (Rfree = 0.000) for 1814 atoms. Found 0 (11 requested) and removed 7 (5 requested) atoms. Cycle 44: After refmac, R = 0.2348 (Rfree = 0.000) for 1807 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. Cycle 45: After refmac, R = 0.2320 (Rfree = 0.000) for 1802 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.54 3.09 Search for helices and strands: 0 residues in 0 chains, 1811 seeds are put forward Round 1: 94 peptides, 20 chains. Longest chain 7 peptides. Score 0.250 Round 2: 95 peptides, 17 chains. Longest chain 11 peptides. Score 0.327 Round 3: 100 peptides, 16 chains. Longest chain 14 peptides. Score 0.376 Round 4: 102 peptides, 18 chains. Longest chain 11 peptides. Score 0.340 Round 5: 103 peptides, 17 chains. Longest chain 10 peptides. Score 0.368 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 84, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence Sequence coverage is 15 % Consider running further cycles of model building using 2gpj-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4295 reflections ( 99.44 % complete ) and 4145 restraints for refining 1827 atoms. 3790 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2390 (Rfree = 0.000) for 1827 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2239 (Rfree = 0.000) for 1819 atoms. Found 0 (11 requested) and removed 2 (5 requested) atoms. Cycle 48: After refmac, R = 0.2235 (Rfree = 0.000) for 1817 atoms. Found 0 (11 requested) and removed 0 (5 requested) atoms. Cycle 49: After refmac, R = 0.2215 (Rfree = 0.000) for 1817 atoms. TimeTaking 32.07