Sun 23 Dec 22:22:43 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 2ogi-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ogi-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ogi-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ogi-4.0-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/2ogi-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ogi-4.0-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 22:22:52 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/2ogi-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ogi-4.0-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 262 and 0 Target number of residues in the AU: 262 Target solvent content: 0.6790 Checking the provided sequence file Detected sequence length: 196 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 392 Adjusted target solvent content: 0.52 Input MTZ file: 2ogi-4.0-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: 4 Cell parameters: 65.860 52.534 70.037 90.000 114.298 90.000 Input sequence file: 2ogi-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 3136 target number of atoms Had to go as low as 0.90 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 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 63.833 4.001 Wilson plot Bfac: 100.06 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 3807 reflections ( 99.76 % complete ) and 0 restraints for refining 3495 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3668 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3082 (Rfree = 0.000) for 3495 atoms. Found 16 (16 requested) and removed 196 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.62 3.52 Search for helices and strands: 0 residues in 0 chains, 3335 seeds are put forward NCS extension: 0 residues added, 3335 seeds are put forward Round 1: 86 peptides, 20 chains. Longest chain 6 peptides. Score 0.198 Round 2: 120 peptides, 22 chains. Longest chain 9 peptides. Score 0.314 Round 3: 130 peptides, 23 chains. Longest chain 9 peptides. Score 0.337 Round 4: 146 peptides, 27 chains. Longest chain 11 peptides. Score 0.332 Round 5: 136 peptides, 25 chains. Longest chain 10 peptides. Score 0.326 Taking the results from Round 3 Chains 23, Residues 107, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3807 reflections ( 99.76 % complete ) and 6935 restraints for refining 2832 atoms. 6530 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2758 (Rfree = 0.000) for 2832 atoms. Found 8 (13 requested) and removed 45 (6 requested) atoms. Cycle 2: After refmac, R = 0.2754 (Rfree = 0.000) for 2765 atoms. Found 13 (13 requested) and removed 32 (6 requested) atoms. Cycle 3: After refmac, R = 0.2807 (Rfree = 0.000) for 2721 atoms. Found 13 (13 requested) and removed 21 (6 requested) atoms. Cycle 4: After refmac, R = 0.2515 (Rfree = 0.000) for 2696 atoms. Found 7 (12 requested) and removed 20 (6 requested) atoms. Cycle 5: After refmac, R = 0.2723 (Rfree = 0.000) for 2672 atoms. Found 12 (12 requested) and removed 21 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.96 3.86 Search for helices and strands: 0 residues in 0 chains, 2769 seeds are put forward NCS extension: 0 residues added, 2769 seeds are put forward Round 1: 136 peptides, 26 chains. Longest chain 12 peptides. Score 0.309 Round 2: 161 peptides, 27 chains. Longest chain 12 peptides. Score 0.390 Round 3: 165 peptides, 24 chains. Longest chain 13 peptides. Score 0.452 Round 4: 170 peptides, 25 chains. Longest chain 14 peptides. Score 0.454 Round 5: 187 peptides, 26 chains. Longest chain 14 peptides. Score 0.496 Taking the results from Round 5 Chains 26, Residues 161, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 3807 reflections ( 99.76 % complete ) and 5833 restraints for refining 2617 atoms. 5173 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2470 (Rfree = 0.000) for 2617 atoms. Found 12 (12 requested) and removed 38 (6 requested) atoms. Cycle 7: After refmac, R = 0.2594 (Rfree = 0.000) for 2565 atoms. Found 12 (12 requested) and removed 24 (6 requested) atoms. Cycle 8: After refmac, R = 0.2050 (Rfree = 0.000) for 2537 atoms. Found 3 (12 requested) and removed 13 (6 requested) atoms. Cycle 9: After refmac, R = 0.2456 (Rfree = 0.000) for 2521 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 10: After refmac, R = 0.2271 (Rfree = 0.000) for 2514 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.97 3.87 Search for helices and strands: 0 residues in 0 chains, 2614 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 2632 seeds are put forward Round 1: 152 peptides, 29 chains. Longest chain 9 peptides. Score 0.322 Round 2: 169 peptides, 26 chains. Longest chain 19 peptides. Score 0.435 Round 3: 176 peptides, 26 chains. Longest chain 17 peptides. Score 0.459 Round 4: 175 peptides, 26 chains. Longest chain 19 peptides. Score 0.456 Round 5: 182 peptides, 28 chains. Longest chain 19 peptides. Score 0.449 Taking the results from Round 3 Chains 27, Residues 150, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3807 reflections ( 99.76 % complete ) and 5908 restraints for refining 2681 atoms. 5284 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2436 (Rfree = 0.000) for 2681 atoms. Found 12 (12 requested) and removed 27 (6 requested) atoms. Cycle 12: After refmac, R = 0.2401 (Rfree = 0.000) for 2642 atoms. Found 12 (12 requested) and removed 22 (6 requested) atoms. Cycle 13: After refmac, R = 0.2413 (Rfree = 0.000) for 2614 atoms. Found 12 (12 requested) and removed 23 (6 requested) atoms. Cycle 14: After refmac, R = 0.2208 (Rfree = 0.000) for 2583 atoms. Found 12 (12 requested) and removed 20 (6 requested) atoms. Cycle 15: After refmac, R = 0.2246 (Rfree = 0.000) for 2562 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.89 3.79 Search for helices and strands: 0 residues in 0 chains, 2671 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 2685 seeds are put forward Round 1: 162 peptides, 32 chains. Longest chain 13 peptides. Score 0.311 Round 2: 174 peptides, 28 chains. Longest chain 11 peptides. Score 0.421 Round 3: 174 peptides, 26 chains. Longest chain 16 peptides. Score 0.452 Round 4: 168 peptides, 23 chains. Longest chain 18 peptides. Score 0.478 Round 5: 171 peptides, 24 chains. Longest chain 16 peptides. Score 0.473 Taking the results from Round 4 Chains 24, Residues 145, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 3807 reflections ( 99.76 % complete ) and 5921 restraints for refining 2703 atoms. 5303 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2385 (Rfree = 0.000) for 2703 atoms. Found 12 (12 requested) and removed 43 (6 requested) atoms. Cycle 17: After refmac, R = 0.2326 (Rfree = 0.000) for 2648 atoms. Found 12 (12 requested) and removed 21 (6 requested) atoms. Cycle 18: After refmac, R = 0.2166 (Rfree = 0.000) for 2623 atoms. Found 10 (12 requested) and removed 19 (6 requested) atoms. Cycle 19: After refmac, R = 0.1725 (Rfree = 0.000) for 2605 atoms. Found 7 (12 requested) and removed 10 (6 requested) atoms. Cycle 20: After refmac, R = 0.1968 (Rfree = 0.000) for 2598 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.92 3.82 Search for helices and strands: 0 residues in 0 chains, 2680 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 2696 seeds are put forward Round 1: 148 peptides, 30 chains. Longest chain 11 peptides. Score 0.288 Round 2: 182 peptides, 31 chains. Longest chain 11 peptides. Score 0.403 Round 3: 184 peptides, 24 chains. Longest chain 20 peptides. Score 0.516 Round 4: 191 peptides, 26 chains. Longest chain 20 peptides. Score 0.509 Round 5: 191 peptides, 28 chains. Longest chain 17 peptides. Score 0.480 Taking the results from Round 3 Chains 26, Residues 160, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 3807 reflections ( 99.76 % complete ) and 5932 restraints for refining 2739 atoms. 5255 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2277 (Rfree = 0.000) for 2739 atoms. Found 13 (13 requested) and removed 46 (6 requested) atoms. Cycle 22: After refmac, R = 0.2137 (Rfree = 0.000) for 2697 atoms. Found 12 (12 requested) and removed 28 (6 requested) atoms. Cycle 23: After refmac, R = 0.2094 (Rfree = 0.000) for 2662 atoms. Found 8 (12 requested) and removed 16 (6 requested) atoms. Cycle 24: After refmac, R = 0.1668 (Rfree = 0.000) for 2645 atoms. Found 5 (12 requested) and removed 9 (6 requested) atoms. Cycle 25: After refmac, R = 0.1608 (Rfree = 0.000) for 2639 atoms. Found 0 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.92 3.82 Search for helices and strands: 0 residues in 0 chains, 2736 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 2750 seeds are put forward Round 1: 135 peptides, 28 chains. Longest chain 10 peptides. Score 0.269 Round 2: 144 peptides, 24 chains. Longest chain 13 peptides. Score 0.375 Round 3: 147 peptides, 22 chains. Longest chain 18 peptides. Score 0.420 Round 4: 150 peptides, 22 chains. Longest chain 15 peptides. Score 0.431 Round 5: 158 peptides, 23 chains. Longest chain 15 peptides. Score 0.443 Taking the results from Round 5 Chains 23, Residues 135, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3807 reflections ( 99.76 % complete ) and 6306 restraints for refining 2733 atoms. 5789 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2213 (Rfree = 0.000) for 2733 atoms. Found 12 (12 requested) and removed 27 (6 requested) atoms. Cycle 27: After refmac, R = 0.2422 (Rfree = 0.000) for 2702 atoms. Found 12 (12 requested) and removed 25 (6 requested) atoms. Cycle 28: After refmac, R = 0.2060 (Rfree = 0.000) for 2672 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 29: After refmac, R = 0.2321 (Rfree = 0.000) for 2657 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 30: After refmac, R = 0.2192 (Rfree = 0.000) for 2641 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.91 3.81 Search for helices and strands: 0 residues in 0 chains, 2725 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 2746 seeds are put forward Round 1: 118 peptides, 24 chains. Longest chain 12 peptides. Score 0.269 Round 2: 143 peptides, 25 chains. Longest chain 16 peptides. Score 0.354 Round 3: 138 peptides, 22 chains. Longest chain 15 peptides. Score 0.386 Round 4: 135 peptides, 20 chains. Longest chain 16 peptides. Score 0.409 Round 5: 137 peptides, 20 chains. Longest chain 16 peptides. Score 0.416 Taking the results from Round 5 Chains 22, Residues 117, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3807 reflections ( 99.76 % complete ) and 5959 restraints for refining 2658 atoms. 5468 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2305 (Rfree = 0.000) for 2658 atoms. Found 12 (12 requested) and removed 21 (6 requested) atoms. Cycle 32: After refmac, R = 0.2198 (Rfree = 0.000) for 2636 atoms. Found 12 (12 requested) and removed 22 (6 requested) atoms. Cycle 33: After refmac, R = 0.2075 (Rfree = 0.000) for 2615 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 34: After refmac, R = 0.2208 (Rfree = 0.000) for 2606 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 35: After refmac, R = 0.2093 (Rfree = 0.000) for 2593 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.89 3.79 Search for helices and strands: 0 residues in 0 chains, 2710 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 2722 seeds are put forward Round 1: 120 peptides, 25 chains. Longest chain 8 peptides. Score 0.259 Round 2: 133 peptides, 24 chains. Longest chain 10 peptides. Score 0.332 Round 3: 123 peptides, 22 chains. Longest chain 10 peptides. Score 0.327 Round 4: 122 peptides, 23 chains. Longest chain 8 peptides. Score 0.304 Round 5: 124 peptides, 23 chains. Longest chain 10 peptides. Score 0.313 Taking the results from Round 2 Chains 24, Residues 109, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3807 reflections ( 99.76 % complete ) and 5900 restraints for refining 2591 atoms. 5488 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2176 (Rfree = 0.000) for 2591 atoms. Found 12 (12 requested) and removed 21 (6 requested) atoms. Cycle 37: After refmac, R = 0.2031 (Rfree = 0.000) for 2572 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 38: After refmac, R = 0.2112 (Rfree = 0.000) for 2569 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 39: After refmac, R = 0.2235 (Rfree = 0.000) for 2557 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 40: After refmac, R = 0.2285 (Rfree = 0.000) for 2542 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.96 3.86 Search for helices and strands: 0 residues in 0 chains, 2620 seeds are put forward NCS extension: 0 residues added, 2620 seeds are put forward Round 1: 98 peptides, 20 chains. Longest chain 8 peptides. Score 0.256 Round 2: 122 peptides, 20 chains. Longest chain 13 peptides. Score 0.358 Round 3: 135 peptides, 22 chains. Longest chain 11 peptides. Score 0.375 Round 4: 131 peptides, 22 chains. Longest chain 13 peptides. Score 0.359 Round 5: 125 peptides, 23 chains. Longest chain 7 peptides. Score 0.317 Taking the results from Round 3 Chains 22, Residues 113, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3807 reflections ( 99.76 % complete ) and 5774 restraints for refining 2561 atoms. 5344 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2114 (Rfree = 0.000) for 2561 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 42: After refmac, R = 0.2192 (Rfree = 0.000) for 2537 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 43: After refmac, R = 0.2018 (Rfree = 0.000) for 2518 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.2050 (Rfree = 0.000) for 2507 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 45: After refmac, R = 0.2140 (Rfree = 0.000) for 2503 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.88 3.78 Search for helices and strands: 0 residues in 0 chains, 2588 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2601 seeds are put forward Round 1: 86 peptides, 19 chains. Longest chain 7 peptides. Score 0.218 Round 2: 111 peptides, 22 chains. Longest chain 8 peptides. Score 0.276 Round 3: 107 peptides, 21 chains. Longest chain 10 peptides. Score 0.277 Round 4: 120 peptides, 20 chains. Longest chain 13 peptides. Score 0.350 Round 5: 116 peptides, 20 chains. Longest chain 8 peptides. Score 0.334 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 100, 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 2ogi-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3807 reflections ( 99.76 % complete ) and 5698 restraints for refining 2515 atoms. 5318 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2242 (Rfree = 0.000) for 2515 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2253 (Rfree = 0.000) for 2488 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2200 (Rfree = 0.000) for 2475 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2513 (Rfree = 0.000) for 2464 atoms. TimeTaking 47.08