Sun 23 Dec 22:22:42 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 2ess-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ess-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ess-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ess-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/2ess-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ess-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 ============================================================ Sun 23 Dec 22:22:56 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/2ess-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ess-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 201 and 0 Target number of residues in the AU: 201 Target solvent content: 0.6499 Checking the provided sequence file Detected sequence length: 248 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 248 Adjusted target solvent content: 0.57 Input MTZ file: 2ess-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: 152 Cell parameters: 91.150 91.150 64.770 90.000 90.000 120.000 Input sequence file: 2ess-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 1984 target number of atoms Had to go as low as 0.85 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: 29.962 3.400 Wilson plot Bfac: 77.68 4474 reflections ( 99.80 % complete ) and 0 restraints for refining 2215 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Starting model: R = 0.3606 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3352 (Rfree = 0.000) for 2215 atoms. Found 15 (16 requested) and removed 22 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.46 3.15 Search for helices and strands: 0 residues in 0 chains, 2234 seeds are put forward Round 1: 94 peptides, 19 chains. Longest chain 8 peptides. Score 0.281 Round 2: 128 peptides, 22 chains. Longest chain 11 peptides. Score 0.399 Round 3: 130 peptides, 19 chains. Longest chain 15 peptides. Score 0.474 Round 4: 139 peptides, 20 chains. Longest chain 15 peptides. Score 0.495 Round 5: 137 peptides, 19 chains. Longest chain 16 peptides. Score 0.507 Taking the results from Round 5 Chains 19, Residues 118, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4474 reflections ( 99.80 % complete ) and 4004 restraints for refining 1804 atoms. 3551 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2926 (Rfree = 0.000) for 1804 atoms. Found 9 (13 requested) and removed 10 (6 requested) atoms. Cycle 2: After refmac, R = 0.2771 (Rfree = 0.000) for 1783 atoms. Found 5 (13 requested) and removed 8 (6 requested) atoms. Cycle 3: After refmac, R = 0.2747 (Rfree = 0.000) for 1768 atoms. Found 1 (13 requested) and removed 6 (6 requested) atoms. Cycle 4: After refmac, R = 0.2741 (Rfree = 0.000) for 1759 atoms. Found 0 (13 requested) and removed 8 (6 requested) atoms. Cycle 5: After refmac, R = 0.2695 (Rfree = 0.000) for 1749 atoms. Found 0 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.45 3.14 Search for helices and strands: 0 residues in 0 chains, 1804 seeds are put forward Round 1: 118 peptides, 21 chains. Longest chain 10 peptides. Score 0.369 Round 2: 135 peptides, 22 chains. Longest chain 13 peptides. Score 0.434 Round 3: 142 peptides, 22 chains. Longest chain 17 peptides. Score 0.468 Round 4: 149 peptides, 24 chains. Longest chain 16 peptides. Score 0.460 Round 5: 143 peptides, 21 chains. Longest chain 16 peptides. Score 0.493 Taking the results from Round 5 Chains 21, Residues 122, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4474 reflections ( 99.80 % complete ) and 4048 restraints for refining 1804 atoms. 3581 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2890 (Rfree = 0.000) for 1804 atoms. Found 9 (13 requested) and removed 8 (6 requested) atoms. Cycle 7: After refmac, R = 0.2747 (Rfree = 0.000) for 1798 atoms. Found 6 (13 requested) and removed 10 (6 requested) atoms. Cycle 8: After refmac, R = 0.2648 (Rfree = 0.000) for 1787 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. Cycle 9: After refmac, R = 0.2672 (Rfree = 0.000) for 1783 atoms. Found 5 (13 requested) and removed 6 (6 requested) atoms. Cycle 10: After refmac, R = 0.2613 (Rfree = 0.000) for 1776 atoms. Found 4 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.48 3.17 Search for helices and strands: 0 residues in 0 chains, 1825 seeds are put forward Round 1: 134 peptides, 25 chains. Longest chain 9 peptides. Score 0.363 Round 2: 139 peptides, 20 chains. Longest chain 12 peptides. Score 0.495 Round 3: 135 peptides, 17 chains. Longest chain 21 peptides. Score 0.538 Round 4: 153 peptides, 18 chains. Longest chain 18 peptides. Score 0.594 Round 5: 138 peptides, 16 chains. Longest chain 25 peptides. Score 0.570 Taking the results from Round 4 Chains 18, Residues 135, Estimated correctness of the model 26.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4474 reflections ( 99.80 % complete ) and 4004 restraints for refining 1804 atoms. 3482 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2812 (Rfree = 0.000) for 1804 atoms. Found 8 (13 requested) and removed 9 (6 requested) atoms. Cycle 12: After refmac, R = 0.2689 (Rfree = 0.000) for 1798 atoms. Found 5 (13 requested) and removed 11 (6 requested) atoms. Cycle 13: After refmac, R = 0.2627 (Rfree = 0.000) for 1790 atoms. Found 3 (13 requested) and removed 10 (6 requested) atoms. Cycle 14: After refmac, R = 0.2510 (Rfree = 0.000) for 1779 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 15: After refmac, R = 0.2438 (Rfree = 0.000) for 1769 atoms. Found 0 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.40 3.10 Search for helices and strands: 0 residues in 0 chains, 1801 seeds are put forward Round 1: 132 peptides, 22 chains. Longest chain 17 peptides. Score 0.419 Round 2: 136 peptides, 19 chains. Longest chain 17 peptides. Score 0.502 Round 3: 143 peptides, 21 chains. Longest chain 14 peptides. Score 0.493 Round 4: 148 peptides, 19 chains. Longest chain 17 peptides. Score 0.555 Round 5: 136 peptides, 18 chains. Longest chain 19 peptides. Score 0.522 Taking the results from Round 4 Chains 20, Residues 129, Estimated correctness of the model 13.3 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4474 reflections ( 99.80 % complete ) and 3931 restraints for refining 1804 atoms. 3398 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2590 (Rfree = 0.000) for 1804 atoms. Found 8 (13 requested) and removed 10 (6 requested) atoms. Cycle 17: After refmac, R = 0.2413 (Rfree = 0.000) for 1794 atoms. Found 1 (13 requested) and removed 7 (6 requested) atoms. Cycle 18: After refmac, R = 0.2860 (Rfree = 0.000) for 1783 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 19: After refmac, R = 0.2393 (Rfree = 0.000) for 1782 atoms. Found 3 (13 requested) and removed 9 (6 requested) atoms. Cycle 20: After refmac, R = 0.2444 (Rfree = 0.000) for 1770 atoms. Found 6 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.37 3.07 Search for helices and strands: 0 residues in 0 chains, 1837 seeds are put forward Round 1: 132 peptides, 24 chains. Longest chain 12 peptides. Score 0.375 Round 2: 142 peptides, 22 chains. Longest chain 13 peptides. Score 0.468 Round 3: 145 peptides, 21 chains. Longest chain 15 peptides. Score 0.503 Round 4: 143 peptides, 20 chains. Longest chain 16 peptides. Score 0.514 Round 5: 144 peptides, 20 chains. Longest chain 17 peptides. Score 0.518 Taking the results from Round 5 Chains 21, Residues 124, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4474 reflections ( 99.80 % complete ) and 3932 restraints for refining 1804 atoms. 3428 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2546 (Rfree = 0.000) for 1804 atoms. Found 7 (13 requested) and removed 12 (6 requested) atoms. Cycle 22: After refmac, R = 0.2551 (Rfree = 0.000) for 1788 atoms. Found 7 (13 requested) and removed 9 (6 requested) atoms. Cycle 23: After refmac, R = 0.2305 (Rfree = 0.000) for 1781 atoms. Found 5 (13 requested) and removed 7 (6 requested) atoms. Cycle 24: After refmac, R = 0.2288 (Rfree = 0.000) for 1779 atoms. Found 3 (13 requested) and removed 7 (6 requested) atoms. Cycle 25: After refmac, R = 0.2176 (Rfree = 0.000) for 1769 atoms. Found 2 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.38 3.08 Search for helices and strands: 0 residues in 0 chains, 1821 seeds are put forward Round 1: 128 peptides, 22 chains. Longest chain 12 peptides. Score 0.399 Round 2: 155 peptides, 24 chains. Longest chain 13 peptides. Score 0.488 Round 3: 140 peptides, 22 chains. Longest chain 16 peptides. Score 0.459 Round 4: 123 peptides, 18 chains. Longest chain 11 peptides. Score 0.462 Round 5: 124 peptides, 16 chains. Longest chain 17 peptides. Score 0.509 Taking the results from Round 5 Chains 16, Residues 108, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4474 reflections ( 99.80 % complete ) and 4113 restraints for refining 1802 atoms. 3697 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2465 (Rfree = 0.000) for 1802 atoms. Found 12 (13 requested) and removed 9 (6 requested) atoms. Cycle 27: After refmac, R = 0.2347 (Rfree = 0.000) for 1797 atoms. Found 5 (13 requested) and removed 7 (6 requested) atoms. Cycle 28: After refmac, R = 0.2145 (Rfree = 0.000) for 1789 atoms. Found 2 (13 requested) and removed 8 (6 requested) atoms. Cycle 29: After refmac, R = 0.2152 (Rfree = 0.000) for 1782 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. Cycle 30: After refmac, R = 0.2159 (Rfree = 0.000) for 1779 atoms. Found 6 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.40 3.10 Search for helices and strands: 0 residues in 0 chains, 1819 seeds are put forward Round 1: 110 peptides, 18 chains. Longest chain 15 peptides. Score 0.396 Round 2: 125 peptides, 17 chains. Longest chain 17 peptides. Score 0.493 Round 3: 125 peptides, 19 chains. Longest chain 15 peptides. Score 0.450 Round 4: 124 peptides, 17 chains. Longest chain 15 peptides. Score 0.488 Round 5: 118 peptides, 15 chains. Longest chain 15 peptides. Score 0.503 Taking the results from Round 5 Chains 16, Residues 103, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4474 reflections ( 99.80 % complete ) and 4048 restraints for refining 1804 atoms. 3622 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2646 (Rfree = 0.000) for 1804 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 32: After refmac, R = 0.2409 (Rfree = 0.000) for 1801 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 33: After refmac, R = 0.2201 (Rfree = 0.000) for 1796 atoms. Found 4 (13 requested) and removed 10 (6 requested) atoms. Cycle 34: After refmac, R = 0.2481 (Rfree = 0.000) for 1785 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Cycle 35: After refmac, R = 0.2030 (Rfree = 0.000) for 1785 atoms. Found 5 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.40 3.10 Search for helices and strands: 0 residues in 0 chains, 1830 seeds are put forward Round 1: 110 peptides, 20 chains. Longest chain 12 peptides. Score 0.349 Round 2: 140 peptides, 24 chains. Longest chain 13 peptides. Score 0.416 Round 3: 131 peptides, 19 chains. Longest chain 15 peptides. Score 0.479 Round 4: 129 peptides, 18 chains. Longest chain 15 peptides. Score 0.490 Round 5: 137 peptides, 22 chains. Longest chain 15 peptides. Score 0.444 Taking the results from Round 4 Chains 18, Residues 111, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4474 reflections ( 99.80 % complete ) and 4097 restraints for refining 1804 atoms. 3671 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2614 (Rfree = 0.000) for 1804 atoms. Found 12 (13 requested) and removed 11 (6 requested) atoms. Cycle 37: After refmac, R = 0.2506 (Rfree = 0.000) for 1796 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 38: After refmac, R = 0.2311 (Rfree = 0.000) for 1792 atoms. Found 3 (13 requested) and removed 8 (6 requested) atoms. Cycle 39: After refmac, R = 0.2394 (Rfree = 0.000) for 1783 atoms. Found 10 (13 requested) and removed 10 (6 requested) atoms. Cycle 40: After refmac, R = 0.2558 (Rfree = 0.000) for 1778 atoms. Found 11 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.34 3.04 Search for helices and strands: 0 residues in 0 chains, 1840 seeds are put forward Round 1: 94 peptides, 19 chains. Longest chain 9 peptides. Score 0.281 Round 2: 96 peptides, 14 chains. Longest chain 16 peptides. Score 0.416 Round 3: 103 peptides, 16 chains. Longest chain 13 peptides. Score 0.405 Round 4: 117 peptides, 17 chains. Longest chain 14 peptides. Score 0.454 Round 5: 119 peptides, 18 chains. Longest chain 12 peptides. Score 0.442 Taking the results from Round 4 Chains 17, Residues 100, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4474 reflections ( 99.80 % complete ) and 4068 restraints for refining 1804 atoms. 3685 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2536 (Rfree = 0.000) for 1804 atoms. Found 12 (13 requested) and removed 8 (6 requested) atoms. Cycle 42: After refmac, R = 0.2367 (Rfree = 0.000) for 1796 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 43: After refmac, R = 0.2280 (Rfree = 0.000) for 1797 atoms. Found 7 (13 requested) and removed 7 (6 requested) atoms. Cycle 44: After refmac, R = 0.2207 (Rfree = 0.000) for 1793 atoms. Found 13 (13 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.2029 (Rfree = 0.000) for 1796 atoms. Found 1 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.35 3.05 Search for helices and strands: 0 residues in 0 chains, 1843 seeds are put forward Round 1: 100 peptides, 20 chains. Longest chain 8 peptides. Score 0.292 Round 2: 110 peptides, 20 chains. Longest chain 10 peptides. Score 0.349 Round 3: 106 peptides, 19 chains. Longest chain 13 peptides. Score 0.350 Round 4: 103 peptides, 16 chains. Longest chain 11 peptides. Score 0.405 Round 5: 112 peptides, 19 chains. Longest chain 11 peptides. Score 0.383 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 87, 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 2ess-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4474 reflections ( 99.80 % complete ) and 4114 restraints for refining 1804 atoms. 3782 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2214 (Rfree = 0.000) for 1804 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2362 (Rfree = 0.000) for 1795 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2628 (Rfree = 0.000) for 1787 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2342 (Rfree = 0.000) for 1776 atoms. TimeTaking 71.48