Sun 23 Dec 22:23:05 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 2gjg-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gjg-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gjg-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gjg-3.2-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/2gjg-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gjg-3.2-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 22:23:15 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/2gjg-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gjg-3.2-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 195 and 0 Target number of residues in the AU: 195 Target solvent content: 0.5803 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: 0.47 Input MTZ file: 2gjg-3.2-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: 5 Cell parameters: 89.350 48.920 57.630 90.000 93.310 90.000 Input sequence file: 2gjg-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1984 target number of atoms Had to go as low as 0.65 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: 28.767 3.201 Wilson plot Bfac: 44.43 4143 reflections ( 98.41 % complete ) and 0 restraints for refining 2206 atoms. Observations/parameters ratio is 0.47 ------------------------------------------------------ Starting model: R = 0.3032 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2855 (Rfree = 0.000) for 2206 atoms. Found 19 (19 requested) and removed 24 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.91 3.03 Search for helices and strands: 0 residues in 0 chains, 2252 seeds are put forward Round 1: 92 peptides, 19 chains. Longest chain 7 peptides. Score 0.286 Round 2: 116 peptides, 22 chains. Longest chain 9 peptides. Score 0.363 Round 3: 130 peptides, 22 chains. Longest chain 12 peptides. Score 0.450 Round 4: 138 peptides, 25 chains. Longest chain 11 peptides. Score 0.422 Round 5: 150 peptides, 24 chains. Longest chain 12 peptides. Score 0.514 Taking the results from Round 5 Chains 24, Residues 126, Estimated correctness of the model 15.7 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 4143 reflections ( 98.41 % complete ) and 3751 restraints for refining 1811 atoms. 3202 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2539 (Rfree = 0.000) for 1811 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. Cycle 2: After refmac, R = 0.2372 (Rfree = 0.000) for 1794 atoms. Found 13 (16 requested) and removed 12 (8 requested) atoms. Cycle 3: After refmac, R = 0.2246 (Rfree = 0.000) for 1789 atoms. Found 5 (16 requested) and removed 10 (8 requested) atoms. Cycle 4: After refmac, R = 0.2230 (Rfree = 0.000) for 1783 atoms. Found 2 (15 requested) and removed 11 (7 requested) atoms. Cycle 5: After refmac, R = 0.2448 (Rfree = 0.000) for 1771 atoms. Found 10 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.90 3.02 Search for helices and strands: 0 residues in 0 chains, 1844 seeds are put forward Round 1: 129 peptides, 24 chains. Longest chain 10 peptides. Score 0.393 Round 2: 141 peptides, 22 chains. Longest chain 14 peptides. Score 0.512 Round 3: 133 peptides, 19 chains. Longest chain 18 peptides. Score 0.539 Round 4: 127 peptides, 20 chains. Longest chain 12 peptides. Score 0.483 Round 5: 144 peptides, 19 chains. Longest chain 16 peptides. Score 0.594 Taking the results from Round 5 Chains 19, Residues 125, Estimated correctness of the model 39.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4143 reflections ( 98.41 % complete ) and 4035 restraints for refining 1811 atoms. 3554 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2492 (Rfree = 0.000) for 1811 atoms. Found 11 (16 requested) and removed 31 (8 requested) atoms. Cycle 7: After refmac, R = 0.2303 (Rfree = 0.000) for 1789 atoms. Found 9 (16 requested) and removed 10 (8 requested) atoms. Cycle 8: After refmac, R = 0.2170 (Rfree = 0.000) for 1785 atoms. Found 2 (16 requested) and removed 9 (8 requested) atoms. Cycle 9: After refmac, R = 0.2125 (Rfree = 0.000) for 1773 atoms. Found 5 (15 requested) and removed 10 (7 requested) atoms. Cycle 10: After refmac, R = 0.2046 (Rfree = 0.000) for 1768 atoms. Found 1 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.89 3.01 Search for helices and strands: 0 residues in 0 chains, 1816 seeds are put forward Round 1: 109 peptides, 16 chains. Longest chain 15 peptides. Score 0.480 Round 2: 140 peptides, 23 chains. Longest chain 15 peptides. Score 0.483 Round 3: 153 peptides, 21 chains. Longest chain 16 peptides. Score 0.595 Round 4: 144 peptides, 18 chains. Longest chain 17 peptides. Score 0.615 Round 5: 143 peptides, 17 chains. Longest chain 18 peptides. Score 0.631 Taking the results from Round 5 Chains 17, Residues 126, Estimated correctness of the model 49.1 % 3 chains (41 residues) have been docked in sequence ------------------------------------------------------ 4143 reflections ( 98.41 % complete ) and 3524 restraints for refining 1810 atoms. 2882 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2549 (Rfree = 0.000) for 1810 atoms. Found 14 (16 requested) and removed 18 (8 requested) atoms. Cycle 12: After refmac, R = 0.2208 (Rfree = 0.000) for 1802 atoms. Found 12 (16 requested) and removed 10 (8 requested) atoms. Cycle 13: After refmac, R = 0.2106 (Rfree = 0.000) for 1800 atoms. Found 3 (16 requested) and removed 9 (8 requested) atoms. Cycle 14: After refmac, R = 0.2069 (Rfree = 0.000) for 1789 atoms. Found 6 (16 requested) and removed 10 (8 requested) atoms. Cycle 15: After refmac, R = 0.2059 (Rfree = 0.000) for 1784 atoms. Found 2 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.92 3.04 Search for helices and strands: 0 residues in 0 chains, 1810 seeds are put forward Round 1: 120 peptides, 18 chains. Longest chain 11 peptides. Score 0.492 Round 2: 133 peptides, 18 chains. Longest chain 22 peptides. Score 0.562 Round 3: 140 peptides, 20 chains. Longest chain 28 peptides. Score 0.553 Round 4: 140 peptides, 18 chains. Longest chain 29 peptides. Score 0.597 Round 5: 146 peptides, 20 chains. Longest chain 30 peptides. Score 0.583 Taking the results from Round 4 Chains 20, Residues 122, Estimated correctness of the model 40.2 % 1 chains (25 residues) have been docked in sequence ------------------------------------------------------ 4143 reflections ( 98.41 % complete ) and 3691 restraints for refining 1810 atoms. 3094 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2361 (Rfree = 0.000) for 1810 atoms. Found 12 (16 requested) and removed 10 (8 requested) atoms. Cycle 17: After refmac, R = 0.2211 (Rfree = 0.000) for 1810 atoms. Found 5 (16 requested) and removed 10 (8 requested) atoms. Cycle 18: After refmac, R = 0.2122 (Rfree = 0.000) for 1803 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. Cycle 19: After refmac, R = 0.2062 (Rfree = 0.000) for 1796 atoms. Found 2 (16 requested) and removed 8 (8 requested) atoms. Cycle 20: After refmac, R = 0.2034 (Rfree = 0.000) for 1789 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.91 3.03 Search for helices and strands: 0 residues in 0 chains, 1821 seeds are put forward Round 1: 127 peptides, 22 chains. Longest chain 15 peptides. Score 0.432 Round 2: 146 peptides, 22 chains. Longest chain 23 peptides. Score 0.539 Round 3: 150 peptides, 20 chains. Longest chain 19 peptides. Score 0.602 Round 4: 145 peptides, 18 chains. Longest chain 37 peptides. Score 0.620 Round 5: 141 peptides, 21 chains. Longest chain 17 peptides. Score 0.535 Taking the results from Round 4 Chains 18, Residues 127, Estimated correctness of the model 46.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4143 reflections ( 98.41 % complete ) and 3971 restraints for refining 1810 atoms. 3481 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2168 (Rfree = 0.000) for 1810 atoms. Found 2 (16 requested) and removed 10 (8 requested) atoms. Cycle 22: After refmac, R = 0.2071 (Rfree = 0.000) for 1801 atoms. Found 7 (16 requested) and removed 8 (8 requested) atoms. Cycle 23: After refmac, R = 0.2032 (Rfree = 0.000) for 1800 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. Cycle 24: After refmac, R = 0.2019 (Rfree = 0.000) for 1795 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. Cycle 25: After refmac, R = 0.2006 (Rfree = 0.000) for 1790 atoms. Found 2 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.89 3.01 Search for helices and strands: 0 residues in 0 chains, 1802 seeds are put forward Round 1: 132 peptides, 22 chains. Longest chain 16 peptides. Score 0.462 Round 2: 149 peptides, 22 chains. Longest chain 17 peptides. Score 0.554 Round 3: 144 peptides, 19 chains. Longest chain 25 peptides. Score 0.594 Round 4: 147 peptides, 18 chains. Longest chain 29 peptides. Score 0.629 Round 5: 147 peptides, 19 chains. Longest chain 27 peptides. Score 0.608 Taking the results from Round 4 Chains 19, Residues 129, Estimated correctness of the model 48.6 % 1 chains (27 residues) have been docked in sequence ------------------------------------------------------ 4143 reflections ( 98.41 % complete ) and 3636 restraints for refining 1811 atoms. 3004 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2275 (Rfree = 0.000) for 1811 atoms. Found 8 (16 requested) and removed 13 (8 requested) atoms. Cycle 27: After refmac, R = 0.2193 (Rfree = 0.000) for 1800 atoms. Found 1 (16 requested) and removed 9 (8 requested) atoms. Cycle 28: After refmac, R = 0.2215 (Rfree = 0.000) for 1789 atoms. Found 5 (16 requested) and removed 10 (8 requested) atoms. Cycle 29: After refmac, R = 0.2131 (Rfree = 0.000) for 1781 atoms. Found 6 (15 requested) and removed 9 (7 requested) atoms. Cycle 30: After refmac, R = 0.2176 (Rfree = 0.000) for 1778 atoms. Found 2 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.91 3.03 Search for helices and strands: 0 residues in 0 chains, 1799 seeds are put forward Round 1: 108 peptides, 19 chains. Longest chain 12 peptides. Score 0.394 Round 2: 129 peptides, 22 chains. Longest chain 10 peptides. Score 0.444 Round 3: 130 peptides, 19 chains. Longest chain 15 peptides. Score 0.523 Round 4: 125 peptides, 19 chains. Longest chain 13 peptides. Score 0.496 Round 5: 133 peptides, 19 chains. Longest chain 13 peptides. Score 0.539 Taking the results from Round 5 Chains 19, Residues 114, Estimated correctness of the model 23.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4143 reflections ( 98.41 % complete ) and 4041 restraints for refining 1810 atoms. 3604 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2321 (Rfree = 0.000) for 1810 atoms. Found 14 (16 requested) and removed 8 (8 requested) atoms. Cycle 32: After refmac, R = 0.2221 (Rfree = 0.000) for 1812 atoms. Found 7 (16 requested) and removed 8 (8 requested) atoms. Cycle 33: After refmac, R = 0.2141 (Rfree = 0.000) for 1811 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. Cycle 34: After refmac, R = 0.2160 (Rfree = 0.000) for 1806 atoms. Found 2 (16 requested) and removed 8 (8 requested) atoms. Cycle 35: After refmac, R = 0.2177 (Rfree = 0.000) for 1800 atoms. Found 2 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.87 2.99 Search for helices and strands: 0 residues in 0 chains, 1822 seeds are put forward Round 1: 97 peptides, 17 chains. Longest chain 13 peptides. Score 0.378 Round 2: 100 peptides, 15 chains. Longest chain 13 peptides. Score 0.453 Round 3: 92 peptides, 15 chains. Longest chain 11 peptides. Score 0.403 Round 4: 96 peptides, 13 chains. Longest chain 13 peptides. Score 0.483 Round 5: 91 peptides, 14 chains. Longest chain 13 peptides. Score 0.424 Taking the results from Round 4 Chains 13, Residues 83, Estimated correctness of the model 5.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4143 reflections ( 98.41 % complete ) and 4175 restraints for refining 1811 atoms. 3856 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2183 (Rfree = 0.000) for 1811 atoms. Found 9 (16 requested) and removed 13 (8 requested) atoms. Cycle 37: After refmac, R = 0.1983 (Rfree = 0.000) for 1803 atoms. Found 10 (16 requested) and removed 10 (8 requested) atoms. Cycle 38: After refmac, R = 0.1948 (Rfree = 0.000) for 1802 atoms. Found 6 (16 requested) and removed 8 (8 requested) atoms. Cycle 39: After refmac, R = 0.1984 (Rfree = 0.000) for 1799 atoms. Found 9 (16 requested) and removed 9 (8 requested) atoms. Cycle 40: After refmac, R = 0.1834 (Rfree = 0.000) for 1796 atoms. Found 3 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.87 2.99 Search for helices and strands: 0 residues in 0 chains, 1818 seeds are put forward Round 1: 96 peptides, 18 chains. Longest chain 13 peptides. Score 0.343 Round 2: 114 peptides, 21 chains. Longest chain 10 peptides. Score 0.378 Round 3: 105 peptides, 18 chains. Longest chain 10 peptides. Score 0.402 Round 4: 114 peptides, 17 chains. Longest chain 14 peptides. Score 0.483 Round 5: 115 peptides, 18 chains. Longest chain 15 peptides. Score 0.464 Taking the results from Round 4 Chains 17, Residues 97, Estimated correctness of the model 5.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4143 reflections ( 98.41 % complete ) and 4015 restraints for refining 1811 atoms. 3644 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1954 (Rfree = 0.000) for 1811 atoms. Found 12 (16 requested) and removed 8 (8 requested) atoms. Cycle 42: After refmac, R = 0.1821 (Rfree = 0.000) for 1812 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. Cycle 43: After refmac, R = 0.1755 (Rfree = 0.000) for 1805 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. Cycle 44: After refmac, R = 0.1683 (Rfree = 0.000) for 1801 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. Cycle 45: After refmac, R = 0.1643 (Rfree = 0.000) for 1796 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.88 3.00 Search for helices and strands: 0 residues in 0 chains, 1807 seeds are put forward Round 1: 88 peptides, 17 chains. Longest chain 9 peptides. Score 0.317 Round 2: 101 peptides, 15 chains. Longest chain 15 peptides. Score 0.459 Round 3: 101 peptides, 18 chains. Longest chain 15 peptides. Score 0.376 Round 4: 99 peptides, 15 chains. Longest chain 15 peptides. Score 0.447 Round 5: 99 peptides, 15 chains. Longest chain 15 peptides. Score 0.447 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 86, 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 2gjg-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4143 reflections ( 98.41 % complete ) and 4126 restraints for refining 1811 atoms. 3797 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1805 (Rfree = 0.000) for 1811 atoms. Found 0 (16 requested) and removed 5 (8 requested) atoms. Cycle 47: After refmac, R = 0.1784 (Rfree = 0.000) for 1805 atoms. Found 0 (16 requested) and removed 4 (8 requested) atoms. Cycle 48: After refmac, R = 0.1750 (Rfree = 0.000) for 1798 atoms. Found 0 (16 requested) and removed 0 (8 requested) atoms. Cycle 49: After refmac, R = 0.1733 (Rfree = 0.000) for 1798 atoms. Found 0 (16 requested) and removed 2 (8 requested) atoms. Writing output files ... TimeTaking 31.58