Tue 25 Dec 19:27:57 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 2o08-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o08-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o08-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o08-3.2-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/2o08-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o08-3.2-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 ============================================================ Tue 25 Dec 19:28:07 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/2o08-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o08-3.2-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 383 and 0 Target number of residues in the AU: 383 Target solvent content: 0.6195 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: 2o08-3.2-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: 20 Cell parameters: 87.690 166.470 74.630 90.000 90.000 90.000 Input sequence file: 2o08-3.2-parrot-hancs.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 3.200 Wilson plot Bfac: 60.77 9177 reflections ( 98.16 % complete ) and 0 restraints for refining 3321 atoms. Observations/parameters ratio is 0.69 ------------------------------------------------------ Starting model: R = 0.3194 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2756 (Rfree = 0.000) for 3321 atoms. Found 29 (29 requested) and removed 35 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.21 2.69 Search for helices and strands: 0 residues in 0 chains, 3388 seeds are put forward NCS extension: 0 residues added, 3388 seeds are put forward Round 1: 234 peptides, 40 chains. Longest chain 10 peptides. Score 0.409 Round 2: 267 peptides, 38 chains. Longest chain 17 peptides. Score 0.522 Round 3: 277 peptides, 33 chains. Longest chain 24 peptides. Score 0.598 Round 4: 287 peptides, 33 chains. Longest chain 22 peptides. Score 0.620 Round 5: 281 peptides, 33 chains. Longest chain 21 peptides. Score 0.607 Taking the results from Round 4 Chains 33, Residues 254, Estimated correctness of the model 46.3 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 9177 reflections ( 98.16 % complete ) and 5411 restraints for refining 2744 atoms. 4337 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2930 (Rfree = 0.000) for 2744 atoms. Found 24 (24 requested) and removed 25 (12 requested) atoms. Cycle 2: After refmac, R = 0.2758 (Rfree = 0.000) for 2713 atoms. Found 24 (24 requested) and removed 15 (12 requested) atoms. Cycle 3: After refmac, R = 0.2670 (Rfree = 0.000) for 2712 atoms. Found 19 (24 requested) and removed 14 (12 requested) atoms. Cycle 4: After refmac, R = 0.2614 (Rfree = 0.000) for 2706 atoms. Found 19 (24 requested) and removed 13 (12 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2578 (Rfree = 0.000) for 2698 atoms. Found 13 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.26 2.73 Search for helices and strands: 0 residues in 0 chains, 2815 seeds are put forward NCS extension: 37 residues added (0 deleted due to clashes), 2852 seeds are put forward Round 1: 285 peptides, 36 chains. Longest chain 20 peptides. Score 0.586 Round 2: 294 peptides, 32 chains. Longest chain 31 peptides. Score 0.644 Round 3: 286 peptides, 30 chains. Longest chain 21 peptides. Score 0.647 Round 4: 289 peptides, 32 chains. Longest chain 20 peptides. Score 0.634 Round 5: 283 peptides, 29 chains. Longest chain 23 peptides. Score 0.650 Taking the results from Round 5 Chains 33, Residues 254, Estimated correctness of the model 53.8 % 2 chains (30 residues) have been docked in sequence ------------------------------------------------------ 9177 reflections ( 98.16 % complete ) and 5408 restraints for refining 2746 atoms. 4300 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2938 (Rfree = 0.000) for 2746 atoms. Found 24 (24 requested) and removed 26 (12 requested) atoms. Cycle 7: After refmac, R = 0.2818 (Rfree = 0.000) for 2714 atoms. Found 18 (24 requested) and removed 20 (12 requested) atoms. Cycle 8: After refmac, R = 0.2650 (Rfree = 0.000) for 2691 atoms. Found 19 (24 requested) and removed 18 (12 requested) atoms. Cycle 9: After refmac, R = 0.2695 (Rfree = 0.000) for 2676 atoms. Found 15 (24 requested) and removed 17 (12 requested) atoms. Cycle 10: After refmac, R = 0.2744 (Rfree = 0.000) for 2657 atoms. Found 23 (23 requested) and removed 18 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.70 3.10 Search for helices and strands: 0 residues in 0 chains, 2803 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 2829 seeds are put forward Round 1: 240 peptides, 37 chains. Longest chain 15 peptides. Score 0.462 Round 2: 255 peptides, 33 chains. Longest chain 17 peptides. Score 0.547 Round 3: 259 peptides, 31 chains. Longest chain 23 peptides. Score 0.578 Round 4: 270 peptides, 33 chains. Longest chain 25 peptides. Score 0.583 Round 5: 259 peptides, 31 chains. Longest chain 33 peptides. Score 0.578 Taking the results from Round 4 Chains 36, Residues 237, Estimated correctness of the model 36.4 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 9177 reflections ( 98.16 % complete ) and 5640 restraints for refining 2746 atoms. 4653 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3054 (Rfree = 0.000) for 2746 atoms. Found 24 (24 requested) and removed 20 (12 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2937 (Rfree = 0.000) for 2723 atoms. Found 24 (24 requested) and removed 29 (12 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.3035 (Rfree = 0.000) for 2701 atoms. Found 24 (24 requested) and removed 19 (12 requested) atoms. Cycle 14: After refmac, R = 0.2904 (Rfree = 0.000) for 2693 atoms. Found 24 (24 requested) and removed 19 (12 requested) atoms. Cycle 15: After refmac, R = 0.2820 (Rfree = 0.000) for 2684 atoms. Found 24 (24 requested) and removed 19 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.92 3.28 Search for helices and strands: 0 residues in 0 chains, 2862 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2877 seeds are put forward Round 1: 220 peptides, 32 chains. Longest chain 16 peptides. Score 0.468 Round 2: 238 peptides, 29 chains. Longest chain 20 peptides. Score 0.550 Round 3: 232 peptides, 28 chains. Longest chain 17 peptides. Score 0.547 Round 4: 226 peptides, 28 chains. Longest chain 25 peptides. Score 0.532 Round 5: 233 peptides, 29 chains. Longest chain 18 peptides. Score 0.538 Taking the results from Round 2 Chains 29, Residues 209, Estimated correctness of the model 26.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 9177 reflections ( 98.16 % complete ) and 5981 restraints for refining 2745 atoms. 5174 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2888 (Rfree = 0.000) for 2745 atoms. Found 24 (24 requested) and removed 16 (12 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2666 (Rfree = 0.000) for 2746 atoms. Found 19 (24 requested) and removed 12 (12 requested) atoms. Cycle 18: After refmac, R = 0.2623 (Rfree = 0.000) for 2746 atoms. Found 10 (24 requested) and removed 15 (12 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2662 (Rfree = 0.000) for 2736 atoms. Found 19 (24 requested) and removed 15 (12 requested) atoms. Cycle 20: After refmac, R = 0.2895 (Rfree = 0.000) for 2736 atoms. Found 24 (24 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.76 3.15 Search for helices and strands: 0 residues in 0 chains, 2885 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 2910 seeds are put forward Round 1: 211 peptides, 35 chains. Longest chain 16 peptides. Score 0.405 Round 2: 236 peptides, 29 chains. Longest chain 24 peptides. Score 0.545 Round 3: 239 peptides, 30 chains. Longest chain 24 peptides. Score 0.541 Round 4: 239 peptides, 30 chains. Longest chain 21 peptides. Score 0.541 Round 5: 241 peptides, 30 chains. Longest chain 24 peptides. Score 0.546 Taking the results from Round 5 Chains 30, Residues 211, Estimated correctness of the model 25.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9177 reflections ( 98.16 % complete ) and 5999 restraints for refining 2746 atoms. 5185 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2995 (Rfree = 0.000) for 2746 atoms. Found 24 (24 requested) and removed 18 (12 requested) atoms. Cycle 22: After refmac, R = 0.2897 (Rfree = 0.000) for 2745 atoms. Found 24 (24 requested) and removed 16 (12 requested) atoms. Cycle 23: After refmac, R = 0.2805 (Rfree = 0.000) for 2750 atoms. Found 13 (24 requested) and removed 17 (12 requested) atoms. Cycle 24: After refmac, R = 0.2743 (Rfree = 0.000) for 2740 atoms. Found 12 (24 requested) and removed 13 (12 requested) atoms. Cycle 25: After refmac, R = 0.2718 (Rfree = 0.000) for 2735 atoms. Found 19 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.38 2.83 Search for helices and strands: 0 residues in 0 chains, 2871 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 2892 seeds are put forward Round 1: 202 peptides, 30 chains. Longest chain 15 peptides. Score 0.443 Round 2: 234 peptides, 31 chains. Longest chain 17 peptides. Score 0.517 Round 3: 249 peptides, 30 chains. Longest chain 18 peptides. Score 0.566 Round 4: 254 peptides, 31 chains. Longest chain 18 peptides. Score 0.567 Round 5: 227 peptides, 29 chains. Longest chain 18 peptides. Score 0.523 Taking the results from Round 4 Chains 32, Residues 223, Estimated correctness of the model 31.9 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 9177 reflections ( 98.16 % complete ) and 5705 restraints for refining 2746 atoms. 4814 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3277 (Rfree = 0.000) for 2746 atoms. Found 24 (24 requested) and removed 24 (12 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.3262 (Rfree = 0.000) for 2722 atoms. Found 24 (24 requested) and removed 40 (12 requested) atoms. Cycle 28: After refmac, R = 0.3055 (Rfree = 0.000) for 2682 atoms. Found 24 (24 requested) and removed 21 (12 requested) atoms. Cycle 29: After refmac, R = 0.3108 (Rfree = 0.000) for 2661 atoms. Found 24 (24 requested) and removed 21 (12 requested) atoms. Cycle 30: After refmac, R = 0.3236 (Rfree = 0.000) for 2647 atoms. Found 23 (23 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 4.27 3.58 Search for helices and strands: 0 residues in 0 chains, 2810 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 2830 seeds are put forward Round 1: 168 peptides, 28 chains. Longest chain 15 peptides. Score 0.367 Round 2: 208 peptides, 30 chains. Longest chain 21 peptides. Score 0.460 Round 3: 207 peptides, 31 chains. Longest chain 19 peptides. Score 0.444 Round 4: 204 peptides, 28 chains. Longest chain 16 peptides. Score 0.474 Round 5: 206 peptides, 29 chains. Longest chain 19 peptides. Score 0.467 Taking the results from Round 4 Chains 28, Residues 176, Estimated correctness of the model 2.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9177 reflections ( 98.16 % complete ) and 6073 restraints for refining 2746 atoms. 5397 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3093 (Rfree = 0.000) for 2746 atoms. Found 24 (24 requested) and removed 15 (12 requested) atoms. Cycle 32: After refmac, R = 0.3044 (Rfree = 0.000) for 2722 atoms. Found 24 (24 requested) and removed 16 (12 requested) atoms. Cycle 33: After refmac, R = 0.2699 (Rfree = 0.000) for 2710 atoms. Found 24 (24 requested) and removed 12 (12 requested) atoms. Cycle 34: After refmac, R = 0.2568 (Rfree = 0.000) for 2718 atoms. Found 13 (24 requested) and removed 13 (12 requested) atoms. Cycle 35: After refmac, R = 0.2536 (Rfree = 0.000) for 2711 atoms. Found 5 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.27 2.74 Search for helices and strands: 0 residues in 0 chains, 2829 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 2843 seeds are put forward Round 1: 151 peptides, 27 chains. Longest chain 13 peptides. Score 0.326 Round 2: 194 peptides, 29 chains. Longest chain 14 peptides. Score 0.433 Round 3: 199 peptides, 31 chains. Longest chain 15 peptides. Score 0.421 Round 4: 208 peptides, 30 chains. Longest chain 18 peptides. Score 0.460 Round 5: 202 peptides, 29 chains. Longest chain 17 peptides. Score 0.455 Taking the results from Round 4 Chains 30, Residues 178, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 9177 reflections ( 98.16 % complete ) and 6009 restraints for refining 2742 atoms. 5327 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3424 (Rfree = 0.000) for 2742 atoms. Found 24 (24 requested) and removed 33 (12 requested) atoms. Cycle 37: After refmac, R = 0.3182 (Rfree = 0.000) for 2708 atoms. Found 24 (24 requested) and removed 33 (12 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.3239 (Rfree = 0.000) for 2680 atoms. Found 24 (24 requested) and removed 29 (12 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.3062 (Rfree = 0.000) for 2658 atoms. Found 24 (24 requested) and removed 19 (12 requested) atoms. Cycle 40: After refmac, R = 0.2703 (Rfree = 0.000) for 2659 atoms. Found 18 (23 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.93 3.29 Search for helices and strands: 0 residues in 0 chains, 2794 seeds are put forward NCS extension: 32 residues added (1 deleted due to clashes), 2826 seeds are put forward Round 1: 165 peptides, 29 chains. Longest chain 11 peptides. Score 0.343 Round 2: 216 peptides, 34 chains. Longest chain 12 peptides. Score 0.432 Round 3: 202 peptides, 31 chains. Longest chain 19 peptides. Score 0.430 Round 4: 200 peptides, 29 chains. Longest chain 23 peptides. Score 0.450 Round 5: 210 peptides, 28 chains. Longest chain 23 peptides. Score 0.490 Taking the results from Round 5 Chains 28, Residues 182, Estimated correctness of the model 8.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9177 reflections ( 98.16 % complete ) and 6031 restraints for refining 2746 atoms. 5331 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2924 (Rfree = 0.000) for 2746 atoms. Found 24 (24 requested) and removed 14 (12 requested) atoms. Cycle 42: After refmac, R = 0.3332 (Rfree = 0.000) for 2748 atoms. Found 24 (24 requested) and removed 21 (12 requested) atoms. Cycle 43: After refmac, R = 0.3076 (Rfree = 0.000) for 2739 atoms. Found 24 (24 requested) and removed 13 (12 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.3196 (Rfree = 0.000) for 2746 atoms. Found 24 (24 requested) and removed 20 (12 requested) atoms. Cycle 45: After refmac, R = 0.2780 (Rfree = 0.000) for 2738 atoms. Found 18 (24 requested) and removed 15 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.77 3.16 Search for helices and strands: 0 residues in 0 chains, 2861 seeds are put forward NCS extension: 35 residues added (3 deleted due to clashes), 2896 seeds are put forward Round 1: 165 peptides, 31 chains. Longest chain 12 peptides. Score 0.315 Round 2: 196 peptides, 27 chains. Longest chain 31 peptides. Score 0.464 Round 3: 184 peptides, 28 chains. Longest chain 20 peptides. Score 0.416 Round 4: 183 peptides, 26 chains. Longest chain 24 peptides. Score 0.440 Round 5: 180 peptides, 24 chains. Longest chain 19 peptides. Score 0.458 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 169, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 2o08-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9177 reflections ( 98.16 % complete ) and 5954 restraints for refining 2746 atoms. 5286 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2996 (Rfree = 0.000) for 2746 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.3127 (Rfree = 0.000) for 2726 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.3154 (Rfree = 0.000) for 2703 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 49: After refmac, R = 0.3123 (Rfree = 0.000) for 2682 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Writing output files ... TimeTaking 56.88