null Sun 23 Dec 22:22:44 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 2itb-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2itb-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2itb-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2itb-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/2itb-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2itb-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 22:22:53 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/2itb-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2itb-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 249 and 0 Target number of residues in the AU: 249 Target solvent content: 0.6277 Checking the provided sequence file Detected sequence length: 206 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 412 Adjusted target solvent content: 0.38 Input MTZ file: 2itb-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: 19 Cell parameters: 61.232 70.168 84.235 90.000 90.000 90.000 Input sequence file: 2itb-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 3296 target number of atoms Had to go as low as 0.60 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: 53.913 3.200 Wilson plot Bfac: 65.30 6334 reflections ( 99.76 % complete ) and 0 restraints for refining 3678 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3407 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3478 (Rfree = 0.000) for 3678 atoms. Found 20 (33 requested) and removed 44 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.20 3.77 Search for helices and strands: 0 residues in 0 chains, 3769 seeds are put forward NCS extension: 0 residues added, 3769 seeds are put forward Round 1: 114 peptides, 25 chains. Longest chain 7 peptides. Score 0.242 Round 2: 145 peptides, 27 chains. Longest chain 11 peptides. Score 0.353 Round 3: 182 peptides, 32 chains. Longest chain 12 peptides. Score 0.423 Round 4: 197 peptides, 29 chains. Longest chain 16 peptides. Score 0.533 Round 5: 194 peptides, 29 chains. Longest chain 16 peptides. Score 0.522 Taking the results from Round 4 Chains 31, Residues 168, Estimated correctness of the model 21.7 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6334 reflections ( 99.76 % complete ) and 6776 restraints for refining 3009 atoms. 6102 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3061 (Rfree = 0.000) for 3009 atoms. Found 18 (27 requested) and removed 18 (13 requested) atoms. Cycle 2: After refmac, R = 0.3148 (Rfree = 0.000) for 2964 atoms. Found 27 (27 requested) and removed 28 (13 requested) atoms. Cycle 3: After refmac, R = 0.2987 (Rfree = 0.000) for 2937 atoms. Found 10 (26 requested) and removed 18 (13 requested) atoms. Cycle 4: After refmac, R = 0.2852 (Rfree = 0.000) for 2921 atoms. Found 16 (26 requested) and removed 21 (13 requested) atoms. Cycle 5: After refmac, R = 0.2876 (Rfree = 0.000) for 2912 atoms. Found 12 (26 requested) and removed 24 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.18 3.74 Search for helices and strands: 0 residues in 0 chains, 3073 seeds are put forward NCS extension: 8 residues added (0 deleted due to clashes), 3081 seeds are put forward Round 1: 147 peptides, 31 chains. Longest chain 10 peptides. Score 0.283 Round 2: 162 peptides, 28 chains. Longest chain 19 peptides. Score 0.410 Round 3: 164 peptides, 26 chains. Longest chain 12 peptides. Score 0.455 Round 4: 165 peptides, 25 chains. Longest chain 14 peptides. Score 0.477 Round 5: 178 peptides, 27 chains. Longest chain 16 peptides. Score 0.494 Taking the results from Round 5 Chains 28, Residues 151, Estimated correctness of the model 9.4 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 6334 reflections ( 99.76 % complete ) and 6014 restraints for refining 2777 atoms. 5394 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2911 (Rfree = 0.000) for 2777 atoms. Found 21 (24 requested) and removed 27 (12 requested) atoms. Cycle 7: After refmac, R = 0.2733 (Rfree = 0.000) for 2758 atoms. Found 17 (24 requested) and removed 20 (12 requested) atoms. Cycle 8: After refmac, R = 0.2727 (Rfree = 0.000) for 2748 atoms. Found 22 (24 requested) and removed 18 (12 requested) atoms. Cycle 9: After refmac, R = 0.2623 (Rfree = 0.000) for 2747 atoms. Found 17 (24 requested) and removed 15 (12 requested) atoms. Cycle 10: After refmac, R = 0.2523 (Rfree = 0.000) for 2746 atoms. Found 13 (24 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.16 3.72 Search for helices and strands: 0 residues in 0 chains, 2906 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 2917 seeds are put forward Round 1: 125 peptides, 26 chains. Longest chain 9 peptides. Score 0.277 Round 2: 168 peptides, 30 chains. Longest chain 9 peptides. Score 0.399 Round 3: 177 peptides, 29 chains. Longest chain 15 peptides. Score 0.455 Round 4: 174 peptides, 29 chains. Longest chain 11 peptides. Score 0.443 Round 5: 181 peptides, 30 chains. Longest chain 15 peptides. Score 0.454 Taking the results from Round 3 Chains 31, Residues 148, Estimated correctness of the model 0.0 % 4 chains (28 residues) have been docked in sequence ------------------------------------------------------ 6334 reflections ( 99.76 % complete ) and 5909 restraints for refining 2811 atoms. 5247 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2710 (Rfree = 0.000) for 2811 atoms. Found 24 (25 requested) and removed 23 (12 requested) atoms. Cycle 12: After refmac, R = 0.2682 (Rfree = 0.000) for 2803 atoms. Found 24 (25 requested) and removed 18 (12 requested) atoms. Cycle 13: After refmac, R = 0.2220 (Rfree = 0.000) for 2805 atoms. Found 8 (25 requested) and removed 16 (12 requested) atoms. Cycle 14: After refmac, R = 0.2218 (Rfree = 0.000) for 2792 atoms. Found 7 (25 requested) and removed 12 (12 requested) atoms. Cycle 15: After refmac, R = 0.2126 (Rfree = 0.000) for 2787 atoms. Found 1 (25 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.18 3.74 Search for helices and strands: 0 residues in 0 chains, 2901 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2917 seeds are put forward Round 1: 151 peptides, 30 chains. Longest chain 11 peptides. Score 0.322 Round 2: 167 peptides, 30 chains. Longest chain 11 peptides. Score 0.395 Round 3: 159 peptides, 28 chains. Longest chain 11 peptides. Score 0.397 Round 4: 172 peptides, 30 chains. Longest chain 12 peptides. Score 0.417 Round 5: 176 peptides, 28 chains. Longest chain 12 peptides. Score 0.469 Taking the results from Round 5 Chains 29, Residues 148, Estimated correctness of the model 1.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 6334 reflections ( 99.76 % complete ) and 6366 restraints for refining 2926 atoms. 5738 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2710 (Rfree = 0.000) for 2926 atoms. Found 17 (26 requested) and removed 28 (13 requested) atoms. Cycle 17: After refmac, R = 0.2746 (Rfree = 0.000) for 2907 atoms. Found 25 (26 requested) and removed 28 (13 requested) atoms. Cycle 18: After refmac, R = 0.2613 (Rfree = 0.000) for 2891 atoms. Found 15 (26 requested) and removed 16 (13 requested) atoms. Cycle 19: After refmac, R = 0.2494 (Rfree = 0.000) for 2880 atoms. Found 13 (25 requested) and removed 17 (12 requested) atoms. Cycle 20: After refmac, R = 0.2121 (Rfree = 0.000) for 2872 atoms. Found 5 (25 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.18 3.74 Search for helices and strands: 0 residues in 0 chains, 2976 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2992 seeds are put forward Round 1: 145 peptides, 31 chains. Longest chain 9 peptides. Score 0.273 Round 2: 179 peptides, 32 chains. Longest chain 9 peptides. Score 0.410 Round 3: 178 peptides, 32 chains. Longest chain 9 peptides. Score 0.406 Round 4: 182 peptides, 32 chains. Longest chain 11 peptides. Score 0.423 Round 5: 182 peptides, 32 chains. Longest chain 13 peptides. Score 0.423 Taking the results from Round 5 Chains 32, Residues 150, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6334 reflections ( 99.76 % complete ) and 6697 restraints for refining 2953 atoms. 6129 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2726 (Rfree = 0.000) for 2953 atoms. Found 23 (26 requested) and removed 28 (13 requested) atoms. Cycle 22: After refmac, R = 0.2725 (Rfree = 0.000) for 2933 atoms. Found 19 (26 requested) and removed 22 (13 requested) atoms. Cycle 23: After refmac, R = 0.2703 (Rfree = 0.000) for 2915 atoms. Found 19 (26 requested) and removed 22 (13 requested) atoms. Cycle 24: After refmac, R = 0.2574 (Rfree = 0.000) for 2904 atoms. Found 22 (26 requested) and removed 18 (13 requested) atoms. Cycle 25: After refmac, R = 0.2160 (Rfree = 0.000) for 2900 atoms. Found 9 (26 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.19 3.75 Search for helices and strands: 0 residues in 0 chains, 3007 seeds are put forward NCS extension: 0 residues added, 3007 seeds are put forward Round 1: 130 peptides, 29 chains. Longest chain 8 peptides. Score 0.240 Round 2: 157 peptides, 31 chains. Longest chain 9 peptides. Score 0.331 Round 3: 156 peptides, 30 chains. Longest chain 10 peptides. Score 0.345 Round 4: 156 peptides, 31 chains. Longest chain 12 peptides. Score 0.326 Round 5: 156 peptides, 28 chains. Longest chain 10 peptides. Score 0.384 Taking the results from Round 5 Chains 28, Residues 128, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6334 reflections ( 99.76 % complete ) and 6696 restraints for refining 2945 atoms. 6212 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2600 (Rfree = 0.000) for 2945 atoms. Found 21 (26 requested) and removed 28 (13 requested) atoms. Cycle 27: After refmac, R = 0.2752 (Rfree = 0.000) for 2926 atoms. Found 23 (26 requested) and removed 22 (13 requested) atoms. Cycle 28: After refmac, R = 0.2660 (Rfree = 0.000) for 2922 atoms. Found 15 (26 requested) and removed 23 (13 requested) atoms. Cycle 29: After refmac, R = 0.2556 (Rfree = 0.000) for 2908 atoms. Found 17 (26 requested) and removed 19 (13 requested) atoms. Cycle 30: After refmac, R = 0.2192 (Rfree = 0.000) for 2903 atoms. Found 7 (26 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.17 3.73 Search for helices and strands: 0 residues in 0 chains, 3015 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3027 seeds are put forward Round 1: 117 peptides, 25 chains. Longest chain 8 peptides. Score 0.258 Round 2: 150 peptides, 28 chains. Longest chain 12 peptides. Score 0.357 Round 3: 151 peptides, 26 chains. Longest chain 15 peptides. Score 0.400 Round 4: 154 peptides, 26 chains. Longest chain 17 peptides. Score 0.413 Round 5: 161 peptides, 26 chains. Longest chain 18 peptides. Score 0.443 Taking the results from Round 5 Chains 26, Residues 135, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 6334 reflections ( 99.76 % complete ) and 6575 restraints for refining 2943 atoms. 6041 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2707 (Rfree = 0.000) for 2943 atoms. Found 26 (26 requested) and removed 25 (13 requested) atoms. Cycle 32: After refmac, R = 0.2760 (Rfree = 0.000) for 2931 atoms. Found 23 (26 requested) and removed 29 (13 requested) atoms. Cycle 33: After refmac, R = 0.2220 (Rfree = 0.000) for 2918 atoms. Found 8 (26 requested) and removed 23 (13 requested) atoms. Cycle 34: After refmac, R = 0.2141 (Rfree = 0.000) for 2898 atoms. Found 8 (26 requested) and removed 15 (13 requested) atoms. Cycle 35: After refmac, R = 0.2621 (Rfree = 0.000) for 2887 atoms. Found 22 (25 requested) and removed 17 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.13 3.68 Search for helices and strands: 0 residues in 0 chains, 3004 seeds are put forward NCS extension: 0 residues added, 3004 seeds are put forward Round 1: 134 peptides, 29 chains. Longest chain 9 peptides. Score 0.260 Round 2: 154 peptides, 30 chains. Longest chain 11 peptides. Score 0.336 Round 3: 153 peptides, 29 chains. Longest chain 8 peptides. Score 0.351 Round 4: 149 peptides, 27 chains. Longest chain 10 peptides. Score 0.372 Round 5: 150 peptides, 26 chains. Longest chain 11 peptides. Score 0.395 Taking the results from Round 5 Chains 26, Residues 124, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6334 reflections ( 99.76 % complete ) and 6515 restraints for refining 2915 atoms. 6045 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2709 (Rfree = 0.000) for 2915 atoms. Found 23 (26 requested) and removed 18 (13 requested) atoms. Cycle 37: After refmac, R = 0.2748 (Rfree = 0.000) for 2915 atoms. Found 24 (26 requested) and removed 16 (13 requested) atoms. Cycle 38: After refmac, R = 0.2749 (Rfree = 0.000) for 2918 atoms. Found 26 (26 requested) and removed 20 (13 requested) atoms. Cycle 39: After refmac, R = 0.2251 (Rfree = 0.000) for 2915 atoms. Found 11 (26 requested) and removed 15 (13 requested) atoms. Cycle 40: After refmac, R = 0.2272 (Rfree = 0.000) for 2906 atoms. Found 12 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.17 3.73 Search for helices and strands: 0 residues in 0 chains, 3025 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 3037 seeds are put forward Round 1: 101 peptides, 23 chains. Longest chain 7 peptides. Score 0.217 Round 2: 120 peptides, 23 chains. Longest chain 9 peptides. Score 0.315 Round 3: 119 peptides, 22 chains. Longest chain 10 peptides. Score 0.331 Round 4: 127 peptides, 24 chains. Longest chain 11 peptides. Score 0.329 Round 5: 119 peptides, 23 chains. Longest chain 9 peptides. Score 0.310 Taking the results from Round 3 Chains 22, Residues 97, Estimated correctness of the model 0.0 % 3 chains (12 residues) have been docked in sequence ------------------------------------------------------ 6334 reflections ( 99.76 % complete ) and 6304 restraints for refining 2859 atoms. 5904 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3029 (Rfree = 0.000) for 2859 atoms. Found 25 (25 requested) and removed 25 (12 requested) atoms. Cycle 42: After refmac, R = 0.2941 (Rfree = 0.000) for 2849 atoms. Found 25 (25 requested) and removed 19 (12 requested) atoms. Cycle 43: After refmac, R = 0.2631 (Rfree = 0.000) for 2841 atoms. Found 25 (25 requested) and removed 16 (12 requested) atoms. Cycle 44: After refmac, R = 0.2647 (Rfree = 0.000) for 2843 atoms. Found 25 (25 requested) and removed 16 (12 requested) atoms. Cycle 45: After refmac, R = 0.2152 (Rfree = 0.000) for 2843 atoms. Found 10 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.17 3.73 Search for helices and strands: 0 residues in 0 chains, 2951 seeds are put forward NCS extension: 0 residues added, 2951 seeds are put forward Round 1: 81 peptides, 19 chains. Longest chain 7 peptides. Score 0.197 Round 2: 83 peptides, 18 chains. Longest chain 6 peptides. Score 0.232 Round 3: 90 peptides, 18 chains. Longest chain 7 peptides. Score 0.271 Round 4: 97 peptides, 19 chains. Longest chain 7 peptides. Score 0.285 Round 5: 101 peptides, 20 chains. Longest chain 9 peptides. Score 0.284 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 78, 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 2itb-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6334 reflections ( 99.76 % complete ) and 5709 restraints for refining 2676 atoms. 5416 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2861 (Rfree = 0.000) for 2676 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.3041 (Rfree = 0.000) for 2657 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.2931 (Rfree = 0.000) for 2643 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.2863 (Rfree = 0.000) for 2629 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:12:10 GMT 2018 Job finished. TimeTaking 49.44 Used memory is bytes: 20117400