Mon 24 Dec 00:13:16 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2o08-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2o08-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2o08-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o08-3.2-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2o08-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o08-3.2-parrot-mrncs ############### 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 00:13:21 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/mrncs/ArpWArp/wArpResults/WorkingDir/2o08-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o08-3.2-parrot-mrncs/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-mrncs.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-mrncs.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 3330 atoms. Observations/parameters ratio is 0.69 ------------------------------------------------------ Starting model: R = 0.3167 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2833 (Rfree = 0.000) for 3330 atoms. Found 29 (29 requested) and removed 27 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.20 2.68 Search for helices and strands: 0 residues in 0 chains, 3418 seeds are put forward NCS extension: 0 residues added, 3418 seeds are put forward Round 1: 246 peptides, 42 chains. Longest chain 11 peptides. Score 0.418 Round 2: 261 peptides, 32 chains. Longest chain 24 peptides. Score 0.572 Round 3: 281 peptides, 31 chains. Longest chain 21 peptides. Score 0.627 Round 4: 279 peptides, 30 chains. Longest chain 22 peptides. Score 0.632 Round 5: 270 peptides, 28 chains. Longest chain 19 peptides. Score 0.633 Taking the results from Round 5 Chains 28, Residues 242, Estimated correctness of the model 49.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9177 reflections ( 98.16 % complete ) and 5708 restraints for refining 2746 atoms. 4768 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3072 (Rfree = 0.000) for 2746 atoms. Found 24 (24 requested) and removed 32 (12 requested) atoms. Cycle 2: After refmac, R = 0.3001 (Rfree = 0.000) for 2710 atoms. Found 24 (24 requested) and removed 20 (12 requested) atoms. Cycle 3: After refmac, R = 0.2659 (Rfree = 0.000) for 2694 atoms. Found 24 (24 requested) and removed 14 (12 requested) atoms. Cycle 4: After refmac, R = 0.2563 (Rfree = 0.000) for 2693 atoms. Found 13 (24 requested) and removed 15 (12 requested) atoms. Cycle 5: After refmac, R = 0.2621 (Rfree = 0.000) for 2680 atoms. Found 24 (24 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.21 2.69 Search for helices and strands: 0 residues in 0 chains, 2823 seeds are put forward NCS extension: 0 residues added, 2823 seeds are put forward Round 1: 229 peptides, 35 chains. Longest chain 18 peptides. Score 0.456 Round 2: 252 peptides, 29 chains. Longest chain 18 peptides. Score 0.583 Round 3: 250 peptides, 27 chains. Longest chain 37 peptides. Score 0.600 Round 4: 254 peptides, 32 chains. Longest chain 20 peptides. Score 0.556 Round 5: 268 peptides, 33 chains. Longest chain 16 peptides. Score 0.578 Taking the results from Round 3 Chains 28, Residues 223, Estimated correctness of the model 41.1 % 1 chains (31 residues) have been docked in sequence ------------------------------------------------------ 9177 reflections ( 98.16 % complete ) and 5543 restraints for refining 2743 atoms. 4544 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2739 (Rfree = 0.000) for 2743 atoms. Found 18 (24 requested) and removed 22 (12 requested) atoms. Cycle 7: After refmac, R = 0.2671 (Rfree = 0.000) for 2720 atoms. Found 20 (24 requested) and removed 16 (12 requested) atoms. Cycle 8: After refmac, R = 0.2607 (Rfree = 0.000) for 2710 atoms. Found 11 (24 requested) and removed 18 (12 requested) atoms. Cycle 9: After refmac, R = 0.2653 (Rfree = 0.000) for 2695 atoms. Found 14 (24 requested) and removed 15 (12 requested) atoms. Cycle 10: After refmac, R = 0.2697 (Rfree = 0.000) for 2685 atoms. Found 24 (24 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.31 2.77 Search for helices and strands: 0 residues in 0 chains, 2811 seeds are put forward NCS extension: 55 residues added (4 deleted due to clashes), 2866 seeds are put forward Round 1: 240 peptides, 36 chains. Longest chain 16 peptides. Score 0.474 Round 2: 264 peptides, 33 chains. Longest chain 27 peptides. Score 0.569 Round 3: 266 peptides, 30 chains. Longest chain 24 peptides. Score 0.605 Round 4: 260 peptides, 32 chains. Longest chain 24 peptides. Score 0.570 Round 5: 269 peptides, 30 chains. Longest chain 25 peptides. Score 0.611 Taking the results from Round 5 Chains 32, Residues 239, Estimated correctness of the model 44.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 9177 reflections ( 98.16 % complete ) and 5571 restraints for refining 2745 atoms. 4563 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3350 (Rfree = 0.000) for 2745 atoms. Found 24 (24 requested) and removed 44 (12 requested) atoms. Cycle 12: After refmac, R = 0.2943 (Rfree = 0.000) for 2692 atoms. Found 22 (24 requested) and removed 23 (12 requested) atoms. Cycle 13: After refmac, R = 0.2923 (Rfree = 0.000) for 2667 atoms. Found 24 (24 requested) and removed 15 (12 requested) atoms. Cycle 14: After refmac, R = 0.2891 (Rfree = 0.000) for 2661 atoms. Found 23 (24 requested) and removed 15 (12 requested) atoms. Cycle 15: After refmac, R = 0.2921 (Rfree = 0.000) for 2654 atoms. Found 23 (23 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.44 2.88 Search for helices and strands: 0 residues in 0 chains, 2787 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 2800 seeds are put forward Round 1: 232 peptides, 37 chains. Longest chain 23 peptides. Score 0.440 Round 2: 281 peptides, 35 chains. Longest chain 23 peptides. Score 0.587 Round 3: 275 peptides, 35 chains. Longest chain 25 peptides. Score 0.573 Round 4: 268 peptides, 32 chains. Longest chain 26 peptides. Score 0.589 Round 5: 260 peptides, 31 chains. Longest chain 21 peptides. Score 0.581 Taking the results from Round 4 Chains 34, Residues 236, Estimated correctness of the model 38.1 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 9177 reflections ( 98.16 % complete ) and 5654 restraints for refining 2746 atoms. 4673 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3106 (Rfree = 0.000) for 2746 atoms. Found 24 (24 requested) and removed 17 (12 requested) atoms. Cycle 17: After refmac, R = 0.3281 (Rfree = 0.000) for 2721 atoms. Found 24 (24 requested) and removed 16 (12 requested) atoms. Cycle 18: After refmac, R = 0.2888 (Rfree = 0.000) for 2694 atoms. Found 21 (24 requested) and removed 16 (12 requested) atoms. Cycle 19: After refmac, R = 0.2866 (Rfree = 0.000) for 2683 atoms. Found 12 (24 requested) and removed 16 (12 requested) atoms. Cycle 20: After refmac, R = 0.3052 (Rfree = 0.000) for 2669 atoms. Found 24 (24 requested) and removed 17 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 4.15 3.48 Search for helices and strands: 0 residues in 0 chains, 2855 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 2874 seeds are put forward Round 1: 200 peptides, 34 chains. Longest chain 14 peptides. Score 0.385 Round 2: 225 peptides, 31 chains. Longest chain 16 peptides. Score 0.494 Round 3: 225 peptides, 32 chains. Longest chain 17 peptides. Score 0.482 Round 4: 230 peptides, 30 chains. Longest chain 15 peptides. Score 0.519 Round 5: 230 peptides, 30 chains. Longest chain 19 peptides. Score 0.519 Taking the results from Round 5 Chains 30, Residues 200, Estimated correctness of the model 17.4 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 9177 reflections ( 98.16 % complete ) and 5768 restraints for refining 2746 atoms. 4917 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3331 (Rfree = 0.000) for 2746 atoms. Found 24 (24 requested) and removed 40 (12 requested) atoms. Cycle 22: After refmac, R = 0.3204 (Rfree = 0.000) for 2711 atoms. Found 24 (24 requested) and removed 27 (12 requested) atoms. Cycle 23: After refmac, R = 0.3058 (Rfree = 0.000) for 2695 atoms. Found 24 (24 requested) and removed 19 (12 requested) atoms. Cycle 24: After refmac, R = 0.2753 (Rfree = 0.000) for 2694 atoms. Found 13 (24 requested) and removed 19 (12 requested) atoms. Cycle 25: After refmac, R = 0.2738 (Rfree = 0.000) for 2682 atoms. Found 19 (24 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.63 3.04 Search for helices and strands: 0 residues in 0 chains, 2814 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 2838 seeds are put forward Round 1: 211 peptides, 34 chains. Longest chain 13 peptides. Score 0.418 Round 2: 238 peptides, 30 chains. Longest chain 28 peptides. Score 0.539 Round 3: 244 peptides, 30 chains. Longest chain 33 peptides. Score 0.554 Round 4: 256 peptides, 34 chains. Longest chain 25 peptides. Score 0.539 Round 5: 255 peptides, 33 chains. Longest chain 31 peptides. Score 0.547 Taking the results from Round 3 Chains 30, Residues 214, Estimated correctness of the model 28.1 % 1 chains (32 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 9177 reflections ( 98.16 % complete ) and 5562 restraints for refining 2746 atoms. 4590 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3181 (Rfree = 0.000) for 2746 atoms. Found 24 (24 requested) and removed 22 (12 requested) atoms. Cycle 27: After refmac, R = 0.2987 (Rfree = 0.000) for 2738 atoms. Found 18 (24 requested) and removed 19 (12 requested) atoms. Cycle 28: After refmac, R = 0.2959 (Rfree = 0.000) for 2731 atoms. Found 7 (24 requested) and removed 16 (12 requested) atoms. Cycle 29: After refmac, R = 0.2973 (Rfree = 0.000) for 2720 atoms. Found 15 (24 requested) and removed 12 (12 requested) atoms. Cycle 30: After refmac, R = 0.2962 (Rfree = 0.000) for 2723 atoms. Found 3 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.46 2.90 Search for helices and strands: 0 residues in 0 chains, 2827 seeds are put forward NCS extension: 33 residues added (2 deleted due to clashes), 2860 seeds are put forward Round 1: 227 peptides, 38 chains. Longest chain 14 peptides. Score 0.413 Round 2: 229 peptides, 32 chains. Longest chain 15 peptides. Score 0.493 Round 3: 246 peptides, 33 chains. Longest chain 18 peptides. Score 0.525 Round 4: 243 peptides, 36 chains. Longest chain 15 peptides. Score 0.482 Round 5: 232 peptides, 35 chains. Longest chain 17 peptides. Score 0.465 Taking the results from Round 3 Chains 33, Residues 213, Estimated correctness of the model 19.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9177 reflections ( 98.16 % complete ) and 6051 restraints for refining 2746 atoms. 5232 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3405 (Rfree = 0.000) for 2746 atoms. Found 24 (24 requested) and removed 17 (12 requested) atoms. Cycle 32: After refmac, R = 0.3215 (Rfree = 0.000) for 2753 atoms. Found 17 (24 requested) and removed 12 (12 requested) atoms. Cycle 33: After refmac, R = 0.3102 (Rfree = 0.000) for 2752 atoms. Found 24 (24 requested) and removed 14 (12 requested) atoms. Cycle 34: After refmac, R = 0.3049 (Rfree = 0.000) for 2754 atoms. Found 24 (24 requested) and removed 16 (12 requested) atoms. Cycle 35: After refmac, R = 0.3077 (Rfree = 0.000) for 2746 atoms. Found 24 (24 requested) and removed 16 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.83 3.21 Search for helices and strands: 0 residues in 0 chains, 2883 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 2905 seeds are put forward Round 1: 191 peptides, 34 chains. Longest chain 12 peptides. Score 0.357 Round 2: 215 peptides, 31 chains. Longest chain 15 peptides. Score 0.467 Round 3: 221 peptides, 31 chains. Longest chain 15 peptides. Score 0.483 Round 4: 219 peptides, 31 chains. Longest chain 23 peptides. Score 0.478 Round 5: 223 peptides, 29 chains. Longest chain 26 peptides. Score 0.512 Taking the results from Round 5 Chains 30, Residues 194, Estimated correctness of the model 15.2 % 1 chains (22 residues) have been docked in sequence ------------------------------------------------------ 9177 reflections ( 98.16 % complete ) and 5718 restraints for refining 2746 atoms. 4876 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3252 (Rfree = 0.000) for 2746 atoms. Found 24 (24 requested) and removed 18 (12 requested) atoms. Cycle 37: After refmac, R = 0.3196 (Rfree = 0.000) for 2732 atoms. Found 19 (24 requested) and removed 14 (12 requested) atoms. Cycle 38: After refmac, R = 0.3079 (Rfree = 0.000) for 2737 atoms. Found 11 (24 requested) and removed 13 (12 requested) atoms. Cycle 39: After refmac, R = 0.2967 (Rfree = 0.000) for 2733 atoms. Found 7 (24 requested) and removed 13 (12 requested) atoms. Cycle 40: After refmac, R = 0.2851 (Rfree = 0.000) for 2723 atoms. Found 5 (24 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.71 3.11 Search for helices and strands: 0 residues in 0 chains, 2806 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 2827 seeds are put forward Round 1: 176 peptides, 34 chains. Longest chain 9 peptides. Score 0.309 Round 2: 196 peptides, 31 chains. Longest chain 10 peptides. Score 0.412 Round 3: 202 peptides, 29 chains. Longest chain 16 peptides. Score 0.455 Round 4: 200 peptides, 29 chains. Longest chain 16 peptides. Score 0.450 Round 5: 207 peptides, 32 chains. Longest chain 17 peptides. Score 0.432 Taking the results from Round 3 Chains 29, Residues 173, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9177 reflections ( 98.16 % complete ) and 6124 restraints for refining 2745 atoms. 5461 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3234 (Rfree = 0.000) for 2745 atoms. Found 24 (24 requested) and removed 14 (12 requested) atoms. Cycle 42: After refmac, R = 0.2973 (Rfree = 0.000) for 2755 atoms. Found 12 (24 requested) and removed 12 (12 requested) atoms. Cycle 43: After refmac, R = 0.2951 (Rfree = 0.000) for 2747 atoms. Found 9 (24 requested) and removed 12 (12 requested) atoms. Cycle 44: After refmac, R = 0.2924 (Rfree = 0.000) for 2743 atoms. Found 4 (24 requested) and removed 12 (12 requested) atoms. Cycle 45: After refmac, R = 0.2915 (Rfree = 0.000) for 2735 atoms. Found 4 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.74 3.13 Search for helices and strands: 0 residues in 0 chains, 2818 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 2845 seeds are put forward Round 1: 172 peptides, 31 chains. Longest chain 10 peptides. Score 0.338 Round 2: 193 peptides, 31 chains. Longest chain 17 peptides. Score 0.403 Round 3: 194 peptides, 32 chains. Longest chain 19 peptides. Score 0.393 Round 4: 212 peptides, 32 chains. Longest chain 24 peptides. Score 0.446 Round 5: 202 peptides, 30 chains. Longest chain 17 peptides. Score 0.443 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 32, Residues 180, 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. 9177 reflections ( 98.16 % complete ) and 6128 restraints for refining 2745 atoms. 5440 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3067 (Rfree = 0.000) for 2745 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.2867 (Rfree = 0.000) for 2723 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.2833 (Rfree = 0.000) for 2705 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 49: After refmac, R = 0.2736 (Rfree = 0.000) for 2691 atoms. TimeTaking 42.28