Sun 23 Dec 22:23:02 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 2hoe-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hoe-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hoe-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hoe-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/2hoe-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hoe-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 22:23:12 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/2hoe-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hoe-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 257 and 0 Target number of residues in the AU: 257 Target solvent content: 0.6466 Checking the provided sequence file Detected sequence length: 380 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 380 Adjusted target solvent content: 0.48 Input MTZ file: 2hoe-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: 151 Cell parameters: 62.599 62.599 173.950 90.000 90.000 120.000 Input sequence file: 2hoe-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 3040 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: 57.983 3.200 Wilson plot Bfac: 75.83 6406 reflections ( 95.81 % complete ) and 0 restraints for refining 3352 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3239 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3192 (Rfree = 0.000) for 3352 atoms. Found 30 (30 requested) and removed 32 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.37 3.46 Search for helices and strands: 0 residues in 0 chains, 3437 seeds are put forward Round 1: 130 peptides, 24 chains. Longest chain 13 peptides. Score 0.333 Round 2: 186 peptides, 23 chains. Longest chain 37 peptides. Score 0.566 Round 3: 210 peptides, 28 chains. Longest chain 20 peptides. Score 0.571 Round 4: 211 peptides, 22 chains. Longest chain 38 peptides. Score 0.655 Round 5: 218 peptides, 24 chains. Longest chain 24 peptides. Score 0.648 Taking the results from Round 4 Chains 22, Residues 189, Estimated correctness of the model 55.0 % 2 chains (40 residues) have been docked in sequence ------------------------------------------------------ 6406 reflections ( 95.81 % complete ) and 5911 restraints for refining 2773 atoms. 5040 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2648 (Rfree = 0.000) for 2773 atoms. Found 21 (24 requested) and removed 51 (12 requested) atoms. Cycle 2: After refmac, R = 0.2431 (Rfree = 0.000) for 2687 atoms. Found 22 (24 requested) and removed 22 (12 requested) atoms. Cycle 3: After refmac, R = 0.2174 (Rfree = 0.000) for 2666 atoms. Found 9 (24 requested) and removed 14 (12 requested) atoms. Cycle 4: After refmac, R = 0.2063 (Rfree = 0.000) for 2654 atoms. Found 5 (23 requested) and removed 18 (11 requested) atoms. Cycle 5: After refmac, R = 0.2123 (Rfree = 0.000) for 2632 atoms. Found 9 (23 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.31 3.40 Search for helices and strands: 0 residues in 0 chains, 2744 seeds are put forward Round 1: 199 peptides, 25 chains. Longest chain 30 peptides. Score 0.579 Round 2: 207 peptides, 23 chains. Longest chain 32 peptides. Score 0.631 Round 3: 216 peptides, 23 chains. Longest chain 46 peptides. Score 0.656 Round 4: 220 peptides, 23 chains. Longest chain 21 peptides. Score 0.666 Round 5: 230 peptides, 25 chains. Longest chain 32 peptides. Score 0.668 Taking the results from Round 5 Chains 29, Residues 205, Estimated correctness of the model 58.1 % 3 chains (33 residues) have been docked in sequence ------------------------------------------------------ 6406 reflections ( 95.81 % complete ) and 5672 restraints for refining 2730 atoms. 4752 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2504 (Rfree = 0.000) for 2730 atoms. Found 10 (24 requested) and removed 27 (12 requested) atoms. Cycle 7: After refmac, R = 0.2308 (Rfree = 0.000) for 2691 atoms. Found 7 (24 requested) and removed 15 (12 requested) atoms. Cycle 8: After refmac, R = 0.2149 (Rfree = 0.000) for 2673 atoms. Found 4 (24 requested) and removed 14 (12 requested) atoms. Cycle 9: After refmac, R = 0.2086 (Rfree = 0.000) for 2663 atoms. Found 3 (23 requested) and removed 14 (11 requested) atoms. Cycle 10: After refmac, R = 0.2008 (Rfree = 0.000) for 2648 atoms. Found 1 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.31 3.40 Search for helices and strands: 0 residues in 0 chains, 2738 seeds are put forward Round 1: 181 peptides, 25 chains. Longest chain 18 peptides. Score 0.518 Round 2: 208 peptides, 21 chains. Longest chain 32 peptides. Score 0.659 Round 3: 201 peptides, 23 chains. Longest chain 32 peptides. Score 0.613 Round 4: 214 peptides, 21 chains. Longest chain 25 peptides. Score 0.675 Round 5: 203 peptides, 21 chains. Longest chain 37 peptides. Score 0.646 Taking the results from Round 4 Chains 25, Residues 193, Estimated correctness of the model 59.7 % 4 chains (68 residues) have been docked in sequence ------------------------------------------------------ 6406 reflections ( 95.81 % complete ) and 5545 restraints for refining 2775 atoms. 4540 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2277 (Rfree = 0.000) for 2775 atoms. Found 19 (24 requested) and removed 49 (12 requested) atoms. Cycle 12: After refmac, R = 0.2160 (Rfree = 0.000) for 2730 atoms. Found 10 (24 requested) and removed 21 (12 requested) atoms. Cycle 13: After refmac, R = 0.1924 (Rfree = 0.000) for 2712 atoms. Found 6 (24 requested) and removed 17 (12 requested) atoms. Cycle 14: After refmac, R = 0.1811 (Rfree = 0.000) for 2700 atoms. Found 6 (24 requested) and removed 16 (12 requested) atoms. Cycle 15: After refmac, R = 0.2040 (Rfree = 0.000) for 2686 atoms. Found 8 (24 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.30 3.39 Search for helices and strands: 0 residues in 0 chains, 2795 seeds are put forward Round 1: 197 peptides, 25 chains. Longest chain 20 peptides. Score 0.572 Round 2: 215 peptides, 28 chains. Longest chain 23 peptides. Score 0.587 Round 3: 219 peptides, 24 chains. Longest chain 46 peptides. Score 0.651 Round 4: 224 peptides, 25 chains. Longest chain 47 peptides. Score 0.652 Round 5: 210 peptides, 25 chains. Longest chain 17 peptides. Score 0.612 Taking the results from Round 4 Chains 29, Residues 199, Estimated correctness of the model 54.3 % 5 chains (53 residues) have been docked in sequence ------------------------------------------------------ 6406 reflections ( 95.81 % complete ) and 5728 restraints for refining 2774 atoms. 4786 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2336 (Rfree = 0.000) for 2774 atoms. Found 18 (24 requested) and removed 38 (12 requested) atoms. Cycle 17: After refmac, R = 0.2271 (Rfree = 0.000) for 2733 atoms. Found 15 (24 requested) and removed 16 (12 requested) atoms. Cycle 18: After refmac, R = 0.1866 (Rfree = 0.000) for 2716 atoms. Found 9 (24 requested) and removed 13 (12 requested) atoms. Cycle 19: After refmac, R = 0.1747 (Rfree = 0.000) for 2708 atoms. Found 2 (24 requested) and removed 13 (12 requested) atoms. Cycle 20: After refmac, R = 0.1607 (Rfree = 0.000) for 2694 atoms. Found 2 (24 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.29 3.38 Search for helices and strands: 0 residues in 0 chains, 2795 seeds are put forward Round 1: 181 peptides, 27 chains. Longest chain 32 peptides. Score 0.487 Round 2: 196 peptides, 25 chains. Longest chain 19 peptides. Score 0.569 Round 3: 198 peptides, 24 chains. Longest chain 22 peptides. Score 0.590 Round 4: 184 peptides, 23 chains. Longest chain 20 peptides. Score 0.560 Round 5: 196 peptides, 23 chains. Longest chain 19 peptides. Score 0.598 Taking the results from Round 5 Chains 25, Residues 173, Estimated correctness of the model 40.5 % 2 chains (28 residues) have been docked in sequence ------------------------------------------------------ 6406 reflections ( 95.81 % complete ) and 5947 restraints for refining 2753 atoms. 5183 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1996 (Rfree = 0.000) for 2753 atoms. Found 13 (24 requested) and removed 34 (12 requested) atoms. Cycle 22: After refmac, R = 0.1721 (Rfree = 0.000) for 2723 atoms. Found 5 (24 requested) and removed 15 (12 requested) atoms. Cycle 23: After refmac, R = 0.1680 (Rfree = 0.000) for 2710 atoms. Found 2 (24 requested) and removed 15 (12 requested) atoms. Cycle 24: After refmac, R = 0.1639 (Rfree = 0.000) for 2695 atoms. Found 4 (24 requested) and removed 14 (12 requested) atoms. Cycle 25: After refmac, R = 0.1676 (Rfree = 0.000) for 2685 atoms. Found 5 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.29 3.38 Search for helices and strands: 0 residues in 0 chains, 2785 seeds are put forward Round 1: 196 peptides, 32 chains. Longest chain 22 peptides. Score 0.461 Round 2: 212 peptides, 26 chains. Longest chain 32 peptides. Score 0.605 Round 3: 208 peptides, 31 chains. Longest chain 21 peptides. Score 0.520 Round 4: 200 peptides, 25 chains. Longest chain 18 peptides. Score 0.582 Round 5: 194 peptides, 27 chains. Longest chain 19 peptides. Score 0.533 Taking the results from Round 2 Chains 28, Residues 186, Estimated correctness of the model 42.4 % 2 chains (33 residues) have been docked in sequence ------------------------------------------------------ 6406 reflections ( 95.81 % complete ) and 5787 restraints for refining 2775 atoms. 4960 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1851 (Rfree = 0.000) for 2775 atoms. Found 13 (24 requested) and removed 30 (12 requested) atoms. Cycle 27: After refmac, R = 0.2071 (Rfree = 0.000) for 2754 atoms. Found 17 (24 requested) and removed 24 (12 requested) atoms. Cycle 28: After refmac, R = 0.1786 (Rfree = 0.000) for 2740 atoms. Found 8 (24 requested) and removed 22 (12 requested) atoms. Cycle 29: After refmac, R = 0.1773 (Rfree = 0.000) for 2720 atoms. Found 14 (24 requested) and removed 18 (12 requested) atoms. Cycle 30: After refmac, R = 0.1528 (Rfree = 0.000) for 2713 atoms. Found 6 (24 requested) and removed 15 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.30 3.39 Search for helices and strands: 0 residues in 0 chains, 2809 seeds are put forward Round 1: 170 peptides, 26 chains. Longest chain 14 peptides. Score 0.462 Round 2: 182 peptides, 26 chains. Longest chain 19 peptides. Score 0.506 Round 3: 179 peptides, 25 chains. Longest chain 23 peptides. Score 0.511 Round 4: 180 peptides, 24 chains. Longest chain 14 peptides. Score 0.531 Round 5: 173 peptides, 24 chains. Longest chain 21 peptides. Score 0.506 Taking the results from Round 4 Chains 26, Residues 156, Estimated correctness of the model 21.1 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 6406 reflections ( 95.81 % complete ) and 6079 restraints for refining 2774 atoms. 5416 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1739 (Rfree = 0.000) for 2774 atoms. Found 12 (24 requested) and removed 19 (12 requested) atoms. Cycle 32: After refmac, R = 0.1624 (Rfree = 0.000) for 2763 atoms. Found 10 (24 requested) and removed 16 (12 requested) atoms. Cycle 33: After refmac, R = 0.1741 (Rfree = 0.000) for 2755 atoms. Found 18 (24 requested) and removed 14 (12 requested) atoms. Cycle 34: After refmac, R = 0.1647 (Rfree = 0.000) for 2754 atoms. Found 10 (24 requested) and removed 19 (12 requested) atoms. Cycle 35: After refmac, R = 0.1468 (Rfree = 0.000) for 2741 atoms. Found 10 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.29 3.38 Search for helices and strands: 0 residues in 0 chains, 2853 seeds are put forward Round 1: 164 peptides, 24 chains. Longest chain 30 peptides. Score 0.473 Round 2: 199 peptides, 22 chains. Longest chain 44 peptides. Score 0.621 Round 3: 197 peptides, 22 chains. Longest chain 33 peptides. Score 0.615 Round 4: 200 peptides, 25 chains. Longest chain 30 peptides. Score 0.582 Round 5: 191 peptides, 25 chains. Longest chain 20 peptides. Score 0.553 Taking the results from Round 2 Failed to save intermediate PDB Chains 24, Residues 177, Estimated correctness of the model 46.6 % 2 chains (33 residues) have been docked in sequence ------------------------------------------------------ 6406 reflections ( 95.81 % complete ) and 5666 restraints for refining 2775 atoms. 4860 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1694 (Rfree = 0.000) for 2775 atoms. Found 15 (24 requested) and removed 21 (12 requested) atoms. Cycle 37: After refmac, R = 0.1570 (Rfree = 0.000) for 2763 atoms. Found 2 (24 requested) and removed 14 (12 requested) atoms. Cycle 38: After refmac, R = 0.1940 (Rfree = 0.000) for 2744 atoms. Found 16 (24 requested) and removed 13 (12 requested) atoms. Cycle 39: After refmac, R = 0.1603 (Rfree = 0.000) for 2742 atoms. Found 5 (24 requested) and removed 14 (12 requested) atoms. Cycle 40: After refmac, R = 0.1594 (Rfree = 0.000) for 2729 atoms. Found 4 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.29 3.38 Search for helices and strands: 0 residues in 0 chains, 2816 seeds are put forward Round 1: 173 peptides, 27 chains. Longest chain 13 peptides. Score 0.457 Round 2: 183 peptides, 22 chains. Longest chain 27 peptides. Score 0.571 Round 3: 188 peptides, 26 chains. Longest chain 30 peptides. Score 0.527 Round 4: 189 peptides, 22 chains. Longest chain 30 peptides. Score 0.590 Round 5: 179 peptides, 20 chains. Longest chain 38 peptides. Score 0.588 Taking the results from Round 4 Chains 25, Residues 167, Estimated correctness of the model 38.3 % 2 chains (31 residues) have been docked in sequence ------------------------------------------------------ 6406 reflections ( 95.81 % complete ) and 5783 restraints for refining 2775 atoms. 5034 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1798 (Rfree = 0.000) for 2775 atoms. Found 18 (24 requested) and removed 23 (12 requested) atoms. Cycle 42: After refmac, R = 0.1784 (Rfree = 0.000) for 2759 atoms. Found 21 (24 requested) and removed 15 (12 requested) atoms. Cycle 43: After refmac, R = 0.1713 (Rfree = 0.000) for 2764 atoms. Found 16 (24 requested) and removed 15 (12 requested) atoms. Cycle 44: After refmac, R = 0.1378 (Rfree = 0.000) for 2762 atoms. Found 3 (24 requested) and removed 13 (12 requested) atoms. Cycle 45: After refmac, R = 0.1377 (Rfree = 0.000) for 2751 atoms. Found 4 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.28 3.37 Search for helices and strands: 0 residues in 0 chains, 2853 seeds are put forward Round 1: 143 peptides, 21 chains. Longest chain 16 peptides. Score 0.443 Round 2: 166 peptides, 19 chains. Longest chain 30 peptides. Score 0.561 Round 3: 166 peptides, 19 chains. Longest chain 45 peptides. Score 0.561 Round 4: 158 peptides, 20 chains. Longest chain 18 peptides. Score 0.517 Round 5: 166 peptides, 21 chains. Longest chain 18 peptides. Score 0.529 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 147, Estimated correctness of the model 30.1 % 2 chains (45 residues) have been docked in sequence Sequence coverage is 30 % Consider running further cycles of model building using 2hoe-3_warpNtrace.pdb as input Building loops using Loopy2018 21 chains (147 residues) following loop building 2 chains (45 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6406 reflections ( 95.81 % complete ) and 5727 restraints for refining 2775 atoms. 4997 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1656 (Rfree = 0.000) for 2775 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.1610 (Rfree = 0.000) for 2758 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.1882 (Rfree = 0.000) for 2744 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 49: After refmac, R = 0.1558 (Rfree = 0.000) for 2730 atoms. TimeTaking 52.02