Mon 24 Dec 07:44:15 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2o08-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2o08-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2o08-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o08-3.4-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2o08-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o08-3.4-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 07:44:20 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/noncs/ArpWArp/wArpResults/WorkingDir/2o08-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o08-3.4-parrot-noncs/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 376 and 0 Target number of residues in the AU: 376 Target solvent content: 0.6264 Checking the provided sequence file Detected sequence length: 188 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 376 Adjusted target solvent content: 0.63 Input MTZ file: 2o08-3.4-parrot-noncs.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: 20 Cell parameters: 87.690 166.470 74.630 90.000 90.000 90.000 Input sequence file: 2o08-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 3008 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: 83.235 3.400 Wilson plot Bfac: 64.48 7673 reflections ( 98.01 % complete ) and 0 restraints for refining 3359 atoms. Observations/parameters ratio is 0.57 ------------------------------------------------------ Starting model: R = 0.3293 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3245 (Rfree = 0.000) for 3359 atoms. Found 25 (25 requested) and removed 24 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.37 2.82 Search for helices and strands: 0 residues in 0 chains, 3461 seeds are put forward NCS extension: 0 residues added, 3461 seeds are put forward Round 1: 188 peptides, 34 chains. Longest chain 11 peptides. Score 0.348 Round 2: 225 peptides, 34 chains. Longest chain 14 peptides. Score 0.457 Round 3: 238 peptides, 36 chains. Longest chain 14 peptides. Score 0.469 Round 4: 222 peptides, 30 chains. Longest chain 17 peptides. Score 0.498 Round 5: 228 peptides, 29 chains. Longest chain 21 peptides. Score 0.525 Taking the results from Round 5 Chains 29, Residues 199, Estimated correctness of the model 2.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7673 reflections ( 98.01 % complete ) and 5919 restraints for refining 2735 atoms. 5152 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3358 (Rfree = 0.000) for 2735 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Cycle 2: After refmac, R = 0.3035 (Rfree = 0.000) for 2686 atoms. Found 20 (20 requested) and removed 21 (10 requested) atoms. Cycle 3: After refmac, R = 0.2938 (Rfree = 0.000) for 2657 atoms. Found 20 (20 requested) and removed 14 (10 requested) atoms. Cycle 4: After refmac, R = 0.2803 (Rfree = 0.000) for 2639 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. Cycle 5: After refmac, R = 0.2747 (Rfree = 0.000) for 2629 atoms. Found 19 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.25 2.72 Search for helices and strands: 0 residues in 0 chains, 2804 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 2825 seeds are put forward Round 1: 214 peptides, 37 chains. Longest chain 14 peptides. Score 0.388 Round 2: 234 peptides, 39 chains. Longest chain 13 peptides. Score 0.421 Round 3: 234 peptides, 32 chains. Longest chain 16 peptides. Score 0.506 Round 4: 235 peptides, 33 chains. Longest chain 17 peptides. Score 0.497 Round 5: 236 peptides, 34 chains. Longest chain 13 peptides. Score 0.487 Taking the results from Round 3 Chains 33, Residues 202, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7673 reflections ( 98.01 % complete ) and 6022 restraints for refining 2735 atoms. 5216 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2920 (Rfree = 0.000) for 2735 atoms. Found 20 (20 requested) and removed 25 (10 requested) atoms. Cycle 7: After refmac, R = 0.2713 (Rfree = 0.000) for 2703 atoms. Found 20 (20 requested) and removed 15 (10 requested) atoms. Cycle 8: After refmac, R = 0.2640 (Rfree = 0.000) for 2694 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Cycle 9: After refmac, R = 0.2675 (Rfree = 0.000) for 2682 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. Cycle 10: After refmac, R = 0.2722 (Rfree = 0.000) for 2673 atoms. Found 20 (20 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.34 2.80 Search for helices and strands: 0 residues in 0 chains, 2839 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 2858 seeds are put forward Round 1: 197 peptides, 37 chains. Longest chain 13 peptides. Score 0.335 Round 2: 221 peptides, 37 chains. Longest chain 15 peptides. Score 0.409 Round 3: 229 peptides, 33 chains. Longest chain 19 peptides. Score 0.481 Round 4: 240 peptides, 37 chains. Longest chain 18 peptides. Score 0.462 Round 5: 228 peptides, 32 chains. Longest chain 17 peptides. Score 0.490 Taking the results from Round 5 Chains 32, Residues 196, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 7673 reflections ( 98.01 % complete ) and 6008 restraints for refining 2735 atoms. 5205 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2961 (Rfree = 0.000) for 2735 atoms. Found 20 (20 requested) and removed 15 (10 requested) atoms. Cycle 12: After refmac, R = 0.2736 (Rfree = 0.000) for 2711 atoms. Found 20 (20 requested) and removed 20 (10 requested) atoms. Cycle 13: After refmac, R = 0.2710 (Rfree = 0.000) for 2697 atoms. Found 20 (20 requested) and removed 12 (10 requested) atoms. Cycle 14: After refmac, R = 0.2678 (Rfree = 0.000) for 2682 atoms. Found 20 (20 requested) and removed 19 (10 requested) atoms. Cycle 15: After refmac, R = 0.2694 (Rfree = 0.000) for 2669 atoms. Found 20 (20 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.31 2.77 Search for helices and strands: 0 residues in 0 chains, 2825 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 2841 seeds are put forward Round 1: 201 peptides, 38 chains. Longest chain 10 peptides. Score 0.335 Round 2: 218 peptides, 34 chains. Longest chain 14 peptides. Score 0.438 Round 3: 223 peptides, 32 chains. Longest chain 19 peptides. Score 0.476 Round 4: 227 peptides, 30 chains. Longest chain 21 peptides. Score 0.511 Round 5: 219 peptides, 28 chains. Longest chain 15 peptides. Score 0.514 Taking the results from Round 5 Chains 30, Residues 191, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 7673 reflections ( 98.01 % complete ) and 5892 restraints for refining 2734 atoms. 5117 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3091 (Rfree = 0.000) for 2734 atoms. Found 20 (20 requested) and removed 17 (10 requested) atoms. Cycle 17: After refmac, R = 0.2981 (Rfree = 0.000) for 2713 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Cycle 18: After refmac, R = 0.2888 (Rfree = 0.000) for 2693 atoms. Found 20 (20 requested) and removed 19 (10 requested) atoms. Cycle 19: After refmac, R = 0.3031 (Rfree = 0.000) for 2676 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2888 (Rfree = 0.000) for 2658 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 2.84 Search for helices and strands: 0 residues in 0 chains, 2798 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 2819 seeds are put forward Round 1: 179 peptides, 31 chains. Longest chain 10 peptides. Score 0.360 Round 2: 198 peptides, 28 chains. Longest chain 24 peptides. Score 0.457 Round 3: 205 peptides, 29 chains. Longest chain 18 peptides. Score 0.464 Round 4: 212 peptides, 29 chains. Longest chain 28 peptides. Score 0.483 Round 5: 225 peptides, 30 chains. Longest chain 19 peptides. Score 0.506 Taking the results from Round 5 Chains 30, Residues 195, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7673 reflections ( 98.01 % complete ) and 5729 restraints for refining 2734 atoms. 4979 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2963 (Rfree = 0.000) for 2734 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. Cycle 22: After refmac, R = 0.2969 (Rfree = 0.000) for 2687 atoms. Found 20 (20 requested) and removed 15 (10 requested) atoms. Cycle 23: After refmac, R = 0.2834 (Rfree = 0.000) for 2661 atoms. Found 20 (20 requested) and removed 14 (10 requested) atoms. Cycle 24: After refmac, R = 0.2874 (Rfree = 0.000) for 2646 atoms. Found 20 (20 requested) and removed 13 (10 requested) atoms. Cycle 25: After refmac, R = 0.2754 (Rfree = 0.000) for 2636 atoms. Found 20 (20 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.71 3.11 Search for helices and strands: 0 residues in 0 chains, 2758 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2775 seeds are put forward Round 1: 195 peptides, 36 chains. Longest chain 12 peptides. Score 0.343 Round 2: 221 peptides, 36 chains. Longest chain 14 peptides. Score 0.421 Round 3: 217 peptides, 32 chains. Longest chain 16 peptides. Score 0.460 Round 4: 218 peptides, 29 chains. Longest chain 21 peptides. Score 0.499 Round 5: 212 peptides, 30 chains. Longest chain 16 peptides. Score 0.471 Taking the results from Round 4 Chains 29, Residues 189, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7673 reflections ( 98.01 % complete ) and 5961 restraints for refining 2734 atoms. 5234 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2748 (Rfree = 0.000) for 2734 atoms. Found 20 (20 requested) and removed 21 (10 requested) atoms. Cycle 27: After refmac, R = 0.2751 (Rfree = 0.000) for 2712 atoms. Found 20 (20 requested) and removed 17 (10 requested) atoms. Cycle 28: After refmac, R = 0.2596 (Rfree = 0.000) for 2694 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Cycle 29: After refmac, R = 0.2568 (Rfree = 0.000) for 2685 atoms. Found 20 (20 requested) and removed 19 (10 requested) atoms. Cycle 30: After refmac, R = 0.2552 (Rfree = 0.000) for 2681 atoms. Found 20 (20 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.59 3.01 Search for helices and strands: 0 residues in 0 chains, 2827 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 2853 seeds are put forward Round 1: 179 peptides, 33 chains. Longest chain 11 peptides. Score 0.333 Round 2: 209 peptides, 32 chains. Longest chain 17 peptides. Score 0.437 Round 3: 213 peptides, 31 chains. Longest chain 14 peptides. Score 0.461 Round 4: 209 peptides, 32 chains. Longest chain 14 peptides. Score 0.437 Round 5: 211 peptides, 28 chains. Longest chain 14 peptides. Score 0.493 Taking the results from Round 5 Chains 28, Residues 183, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7673 reflections ( 98.01 % complete ) and 5791 restraints for refining 2735 atoms. 5087 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2818 (Rfree = 0.000) for 2735 atoms. Found 20 (20 requested) and removed 13 (10 requested) atoms. Cycle 32: After refmac, R = 0.2752 (Rfree = 0.000) for 2729 atoms. Found 20 (20 requested) and removed 13 (10 requested) atoms. Cycle 33: After refmac, R = 0.2639 (Rfree = 0.000) for 2717 atoms. Found 20 (20 requested) and removed 13 (10 requested) atoms. Cycle 34: After refmac, R = 0.2615 (Rfree = 0.000) for 2712 atoms. Found 20 (20 requested) and removed 14 (10 requested) atoms. Cycle 35: After refmac, R = 0.2620 (Rfree = 0.000) for 2705 atoms. Found 20 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.52 2.95 Search for helices and strands: 0 residues in 0 chains, 2825 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 2836 seeds are put forward Round 1: 182 peptides, 35 chains. Longest chain 15 peptides. Score 0.315 Round 2: 205 peptides, 29 chains. Longest chain 15 peptides. Score 0.464 Round 3: 220 peptides, 37 chains. Longest chain 14 peptides. Score 0.406 Round 4: 215 peptides, 31 chains. Longest chain 14 peptides. Score 0.467 Round 5: 225 peptides, 32 chains. Longest chain 14 peptides. Score 0.482 Taking the results from Round 5 Chains 32, Residues 193, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7673 reflections ( 98.01 % complete ) and 5932 restraints for refining 2734 atoms. 5192 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2954 (Rfree = 0.000) for 2734 atoms. Found 20 (20 requested) and removed 19 (10 requested) atoms. Cycle 37: After refmac, R = 0.2773 (Rfree = 0.000) for 2705 atoms. Found 20 (20 requested) and removed 13 (10 requested) atoms. Cycle 38: After refmac, R = 0.2494 (Rfree = 0.000) for 2703 atoms. Found 17 (20 requested) and removed 12 (10 requested) atoms. Cycle 39: After refmac, R = 0.2408 (Rfree = 0.000) for 2700 atoms. Found 7 (20 requested) and removed 10 (10 requested) atoms. Cycle 40: After refmac, R = 0.2410 (Rfree = 0.000) for 2696 atoms. Found 4 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.35 2.81 Search for helices and strands: 0 residues in 0 chains, 2798 seeds are put forward NCS extension: 0 residues added, 2798 seeds are put forward Round 1: 177 peptides, 33 chains. Longest chain 13 peptides. Score 0.326 Round 2: 193 peptides, 27 chains. Longest chain 14 peptides. Score 0.456 Round 3: 201 peptides, 32 chains. Longest chain 13 peptides. Score 0.414 Round 4: 206 peptides, 30 chains. Longest chain 13 peptides. Score 0.454 Round 5: 203 peptides, 33 chains. Longest chain 12 peptides. Score 0.407 Taking the results from Round 2 Chains 27, Residues 166, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7673 reflections ( 98.01 % complete ) and 5976 restraints for refining 2735 atoms. 5339 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2925 (Rfree = 0.000) for 2735 atoms. Found 20 (20 requested) and removed 17 (10 requested) atoms. Cycle 42: After refmac, R = 0.2607 (Rfree = 0.000) for 2719 atoms. Found 20 (20 requested) and removed 14 (10 requested) atoms. Cycle 43: After refmac, R = 0.2569 (Rfree = 0.000) for 2710 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. Cycle 44: After refmac, R = 0.2533 (Rfree = 0.000) for 2704 atoms. Found 20 (20 requested) and removed 11 (10 requested) atoms. Cycle 45: After refmac, R = 0.2497 (Rfree = 0.000) for 2703 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.36 2.81 Search for helices and strands: 0 residues in 0 chains, 2825 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2840 seeds are put forward Round 1: 172 peptides, 35 chains. Longest chain 13 peptides. Score 0.281 Round 2: 198 peptides, 36 chains. Longest chain 14 peptides. Score 0.352 Round 3: 204 peptides, 35 chains. Longest chain 12 peptides. Score 0.384 Round 4: 212 peptides, 33 chains. Longest chain 13 peptides. Score 0.433 Round 5: 208 peptides, 36 chains. Longest chain 14 peptides. Score 0.383 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 179, 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 2o08-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7673 reflections ( 98.01 % complete ) and 5857 restraints for refining 2735 atoms. 5174 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2861 (Rfree = 0.000) for 2735 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.3039 (Rfree = 0.000) for 2709 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.2747 (Rfree = 0.000) for 2687 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.2695 (Rfree = 0.000) for 2671 atoms. TimeTaking 35.28