null Sun 23 Dec 22:22:56 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-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ess-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ess-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ess-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/2ess-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ess-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 22:23:06 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-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ess-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 206 and 0 Target number of residues in the AU: 206 Target solvent content: 0.6412 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-3.2-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: 152 Cell parameters: 91.150 91.150 64.770 90.000 90.000 120.000 Input sequence file: 2ess-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 0.85 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 3.200 Wilson plot Bfac: 71.90 5352 reflections ( 99.83 % complete ) and 0 restraints for refining 2193 atoms. Observations/parameters ratio is 0.61 ------------------------------------------------------ Starting model: R = 0.3599 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3383 (Rfree = 0.000) for 2193 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.26 2.97 Search for helices and strands: 0 residues in 0 chains, 2221 seeds are put forward Round 1: 106 peptides, 21 chains. Longest chain 10 peptides. Score 0.302 Round 2: 128 peptides, 18 chains. Longest chain 17 peptides. Score 0.486 Round 3: 141 peptides, 18 chains. Longest chain 22 peptides. Score 0.544 Round 4: 152 peptides, 17 chains. Longest chain 20 peptides. Score 0.608 Round 5: 156 peptides, 16 chains. Longest chain 21 peptides. Score 0.640 Taking the results from Round 5 Chains 16, Residues 140, Estimated correctness of the model 51.4 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 5352 reflections ( 99.83 % complete ) and 3814 restraints for refining 1811 atoms. 3203 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3124 (Rfree = 0.000) for 1811 atoms. Found 10 (16 requested) and removed 14 (8 requested) atoms. Cycle 2: After refmac, R = 0.3049 (Rfree = 0.000) for 1774 atoms. Found 10 (16 requested) and removed 16 (8 requested) atoms. Cycle 3: After refmac, R = 0.3064 (Rfree = 0.000) for 1754 atoms. Found 9 (15 requested) and removed 13 (7 requested) atoms. Cycle 4: After refmac, R = 0.2748 (Rfree = 0.000) for 1738 atoms. Found 3 (15 requested) and removed 10 (7 requested) atoms. Cycle 5: After refmac, R = 0.2707 (Rfree = 0.000) for 1727 atoms. Found 6 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.42 3.11 Search for helices and strands: 0 residues in 0 chains, 1760 seeds are put forward Round 1: 141 peptides, 21 chains. Longest chain 19 peptides. Score 0.484 Round 2: 154 peptides, 18 chains. Longest chain 30 peptides. Score 0.598 Round 3: 166 peptides, 21 chains. Longest chain 16 peptides. Score 0.591 Round 4: 163 peptides, 19 chains. Longest chain 33 peptides. Score 0.615 Round 5: 162 peptides, 18 chains. Longest chain 26 peptides. Score 0.628 Taking the results from Round 5 Chains 20, Residues 144, Estimated correctness of the model 48.4 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 5352 reflections ( 99.83 % complete ) and 3701 restraints for refining 1810 atoms. 3077 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3092 (Rfree = 0.000) for 1810 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 7: After refmac, R = 0.2999 (Rfree = 0.000) for 1797 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 8: After refmac, R = 0.2682 (Rfree = 0.000) for 1787 atoms. Found 10 (16 requested) and removed 11 (8 requested) atoms. Cycle 9: After refmac, R = 0.2587 (Rfree = 0.000) for 1779 atoms. Found 7 (16 requested) and removed 11 (8 requested) atoms. Cycle 10: After refmac, R = 0.2777 (Rfree = 0.000) for 1768 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.73 3.40 Search for helices and strands: 0 residues in 0 chains, 1812 seeds are put forward Round 1: 142 peptides, 21 chains. Longest chain 32 peptides. Score 0.489 Round 2: 157 peptides, 20 chains. Longest chain 28 peptides. Score 0.573 Round 3: 160 peptides, 19 chains. Longest chain 29 peptides. Score 0.603 Round 4: 154 peptides, 18 chains. Longest chain 26 peptides. Score 0.598 Round 5: 154 peptides, 17 chains. Longest chain 34 peptides. Score 0.615 Taking the results from Round 5 Chains 17, Residues 137, Estimated correctness of the model 45.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5352 reflections ( 99.83 % complete ) and 3896 restraints for refining 1809 atoms. 3365 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3078 (Rfree = 0.000) for 1809 atoms. Found 15 (16 requested) and removed 15 (8 requested) atoms. Cycle 12: After refmac, R = 0.2985 (Rfree = 0.000) for 1797 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 13: After refmac, R = 0.2799 (Rfree = 0.000) for 1787 atoms. Found 15 (16 requested) and removed 11 (8 requested) atoms. Cycle 14: After refmac, R = 0.2700 (Rfree = 0.000) for 1781 atoms. Found 16 (16 requested) and removed 24 (8 requested) atoms. Cycle 15: After refmac, R = 0.2616 (Rfree = 0.000) for 1772 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.25 2.96 Search for helices and strands: 0 residues in 0 chains, 1842 seeds are put forward Round 1: 134 peptides, 20 chains. Longest chain 12 peptides. Score 0.472 Round 2: 155 peptides, 21 chains. Longest chain 17 peptides. Score 0.547 Round 3: 145 peptides, 17 chains. Longest chain 33 peptides. Score 0.580 Round 4: 164 peptides, 18 chains. Longest chain 28 peptides. Score 0.635 Round 5: 163 peptides, 22 chains. Longest chain 16 peptides. Score 0.561 Taking the results from Round 4 Chains 18, Residues 146, Estimated correctness of the model 50.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5352 reflections ( 99.83 % complete ) and 3762 restraints for refining 1793 atoms. 3196 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2689 (Rfree = 0.000) for 1793 atoms. Found 10 (16 requested) and removed 8 (8 requested) atoms. Cycle 17: After refmac, R = 0.2596 (Rfree = 0.000) for 1789 atoms. Found 7 (16 requested) and removed 10 (8 requested) atoms. Cycle 18: After refmac, R = 0.2388 (Rfree = 0.000) for 1779 atoms. Found 4 (16 requested) and removed 9 (8 requested) atoms. Cycle 19: After refmac, R = 0.2572 (Rfree = 0.000) for 1773 atoms. Found 11 (15 requested) and removed 9 (7 requested) atoms. Cycle 20: After refmac, R = 0.2274 (Rfree = 0.000) for 1772 atoms. Found 6 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.26 2.97 Search for helices and strands: 0 residues in 0 chains, 1825 seeds are put forward Round 1: 138 peptides, 21 chains. Longest chain 15 peptides. Score 0.470 Round 2: 158 peptides, 18 chains. Longest chain 26 peptides. Score 0.613 Round 3: 152 peptides, 20 chains. Longest chain 17 peptides. Score 0.553 Round 4: 161 peptides, 20 chains. Longest chain 29 peptides. Score 0.589 Round 5: 162 peptides, 20 chains. Longest chain 22 peptides. Score 0.593 Taking the results from Round 2 Chains 18, Residues 140, Estimated correctness of the model 44.5 % 3 chains (19 residues) have been docked in sequence ------------------------------------------------------ 5352 reflections ( 99.83 % complete ) and 3720 restraints for refining 1811 atoms. 3106 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2642 (Rfree = 0.000) for 1811 atoms. Found 7 (16 requested) and removed 16 (8 requested) atoms. Cycle 22: After refmac, R = 0.2623 (Rfree = 0.000) for 1797 atoms. Found 10 (16 requested) and removed 10 (8 requested) atoms. Cycle 23: After refmac, R = 0.2475 (Rfree = 0.000) for 1790 atoms. Found 11 (16 requested) and removed 10 (8 requested) atoms. Cycle 24: After refmac, R = 0.2288 (Rfree = 0.000) for 1789 atoms. Found 4 (16 requested) and removed 9 (8 requested) atoms. Cycle 25: After refmac, R = 0.2641 (Rfree = 0.000) for 1781 atoms. Found 12 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.27 2.98 Search for helices and strands: 0 residues in 0 chains, 1840 seeds are put forward Round 1: 129 peptides, 23 chains. Longest chain 12 peptides. Score 0.382 Round 2: 135 peptides, 17 chains. Longest chain 27 peptides. Score 0.538 Round 3: 147 peptides, 22 chains. Longest chain 20 peptides. Score 0.492 Round 4: 152 peptides, 19 chains. Longest chain 21 peptides. Score 0.572 Round 5: 135 peptides, 15 chains. Longest chain 21 peptides. Score 0.577 Taking the results from Round 5 Chains 15, Residues 120, Estimated correctness of the model 34.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5352 reflections ( 99.83 % complete ) and 3877 restraints for refining 1810 atoms. 3412 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2623 (Rfree = 0.000) for 1810 atoms. Found 10 (16 requested) and removed 8 (8 requested) atoms. Cycle 27: After refmac, R = 0.2583 (Rfree = 0.000) for 1809 atoms. Found 10 (16 requested) and removed 9 (8 requested) atoms. Cycle 28: After refmac, R = 0.2314 (Rfree = 0.000) for 1802 atoms. Found 1 (16 requested) and removed 8 (8 requested) atoms. Cycle 29: After refmac, R = 0.2284 (Rfree = 0.000) for 1792 atoms. Found 2 (16 requested) and removed 9 (8 requested) atoms. Cycle 30: After refmac, R = 0.2515 (Rfree = 0.000) for 1783 atoms. Found 11 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.26 2.97 Search for helices and strands: 0 residues in 0 chains, 1836 seeds are put forward Round 1: 113 peptides, 19 chains. Longest chain 13 peptides. Score 0.388 Round 2: 132 peptides, 18 chains. Longest chain 20 peptides. Score 0.504 Round 3: 138 peptides, 19 chains. Longest chain 27 peptides. Score 0.511 Round 4: 138 peptides, 17 chains. Longest chain 27 peptides. Score 0.551 Round 5: 134 peptides, 18 chains. Longest chain 20 peptides. Score 0.513 Taking the results from Round 4 Chains 17, Residues 121, Estimated correctness of the model 27.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5352 reflections ( 99.83 % complete ) and 3843 restraints for refining 1806 atoms. 3376 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2484 (Rfree = 0.000) for 1806 atoms. Found 12 (16 requested) and removed 10 (8 requested) atoms. Cycle 32: After refmac, R = 0.2532 (Rfree = 0.000) for 1803 atoms. Found 16 (16 requested) and removed 9 (8 requested) atoms. Cycle 33: After refmac, R = 0.2564 (Rfree = 0.000) for 1803 atoms. Found 16 (16 requested) and removed 9 (8 requested) atoms. Cycle 34: After refmac, R = 0.2947 (Rfree = 0.000) for 1802 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. Cycle 35: After refmac, R = 0.2390 (Rfree = 0.000) for 1804 atoms. Found 13 (16 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.30 3.00 Search for helices and strands: 0 residues in 0 chains, 1874 seeds are put forward Round 1: 115 peptides, 20 chains. Longest chain 13 peptides. Score 0.376 Round 2: 127 peptides, 15 chains. Longest chain 22 peptides. Score 0.543 Round 3: 146 peptides, 20 chains. Longest chain 15 peptides. Score 0.527 Round 4: 149 peptides, 22 chains. Longest chain 15 peptides. Score 0.501 Round 5: 142 peptides, 19 chains. Longest chain 15 peptides. Score 0.529 Taking the results from Round 2 Chains 15, Residues 112, Estimated correctness of the model 24.8 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 5352 reflections ( 99.83 % complete ) and 3817 restraints for refining 1811 atoms. 3363 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2414 (Rfree = 0.000) for 1811 atoms. Found 9 (16 requested) and removed 29 (8 requested) atoms. Cycle 37: After refmac, R = 0.2445 (Rfree = 0.000) for 1787 atoms. Found 10 (16 requested) and removed 9 (8 requested) atoms. Cycle 38: After refmac, R = 0.2393 (Rfree = 0.000) for 1784 atoms. Found 12 (16 requested) and removed 12 (8 requested) atoms. Cycle 39: After refmac, R = 0.2222 (Rfree = 0.000) for 1780 atoms. Found 4 (15 requested) and removed 7 (7 requested) atoms. Cycle 40: After refmac, R = 0.2208 (Rfree = 0.000) for 1774 atoms. Found 4 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.26 2.97 Search for helices and strands: 0 residues in 0 chains, 1833 seeds are put forward Round 1: 126 peptides, 20 chains. Longest chain 24 peptides. Score 0.433 Round 2: 138 peptides, 21 chains. Longest chain 21 peptides. Score 0.470 Round 3: 135 peptides, 20 chains. Longest chain 21 peptides. Score 0.477 Round 4: 135 peptides, 19 chains. Longest chain 13 peptides. Score 0.498 Round 5: 135 peptides, 19 chains. Longest chain 21 peptides. Score 0.498 Taking the results from Round 5 Chains 19, Residues 116, Estimated correctness of the model 10.7 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 5352 reflections ( 99.83 % complete ) and 3630 restraints for refining 1811 atoms. 3111 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2415 (Rfree = 0.000) for 1811 atoms. Found 15 (16 requested) and removed 13 (8 requested) atoms. Cycle 42: After refmac, R = 0.2285 (Rfree = 0.000) for 1801 atoms. Found 5 (16 requested) and removed 9 (8 requested) atoms. Cycle 43: After refmac, R = 0.2278 (Rfree = 0.000) for 1796 atoms. Found 5 (16 requested) and removed 9 (8 requested) atoms. Cycle 44: After refmac, R = 0.2256 (Rfree = 0.000) for 1792 atoms. Found 7 (16 requested) and removed 8 (8 requested) atoms. Cycle 45: After refmac, R = 0.2653 (Rfree = 0.000) for 1786 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.25 2.96 Search for helices and strands: 0 residues in 0 chains, 1828 seeds are put forward Round 1: 121 peptides, 18 chains. Longest chain 21 peptides. Score 0.452 Round 2: 132 peptides, 18 chains. Longest chain 15 peptides. Score 0.504 Round 3: 135 peptides, 16 chains. Longest chain 22 peptides. Score 0.558 Round 4: 133 peptides, 16 chains. Longest chain 20 peptides. Score 0.549 Round 5: 140 peptides, 21 chains. Longest chain 14 peptides. Score 0.479 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 119, Estimated correctness of the model 29.2 % 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. 5352 reflections ( 99.83 % complete ) and 3731 restraints for refining 1807 atoms. 3271 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2518 (Rfree = 0.000) for 1807 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2440 (Rfree = 0.000) for 1795 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2321 (Rfree = 0.000) for 1783 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2300 (Rfree = 0.000) for 1772 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:06:06 GMT 2018 Job finished. TimeTaking 43.17 Used memory is bytes: 14743856