Mon 24 Dec 07:39:19 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 2p97-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2p97-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2p97-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p97-3.8-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/2p97-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p97-3.8-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 07:39:23 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/2p97-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p97-3.8-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 334 and 0 Target number of residues in the AU: 334 Target solvent content: 0.6462 Checking the provided sequence file Detected sequence length: 201 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 402 Adjusted target solvent content: 0.57 Input MTZ file: 2p97-3.8-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: 94 Cell parameters: 103.080 103.080 96.168 90.000 90.000 90.000 Input sequence file: 2p97-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 3216 target number of atoms Had to go as low as 0.85 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: 72.889 3.800 Wilson plot Bfac: 75.43 5456 reflections ( 99.67 % complete ) and 0 restraints for refining 3545 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3442 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3292 (Rfree = 0.000) for 3545 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.54 3.22 Search for helices and strands: 0 residues in 0 chains, 3610 seeds are put forward NCS extension: 0 residues added, 3610 seeds are put forward Round 1: 193 peptides, 32 chains. Longest chain 12 peptides. Score 0.401 Round 2: 244 peptides, 30 chains. Longest chain 19 peptides. Score 0.571 Round 3: 256 peptides, 28 chains. Longest chain 25 peptides. Score 0.621 Round 4: 259 peptides, 27 chains. Longest chain 18 peptides. Score 0.639 Round 5: 266 peptides, 31 chains. Longest chain 19 peptides. Score 0.613 Taking the results from Round 4 Chains 27, Residues 232, Estimated correctness of the model 16.2 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 5456 reflections ( 99.67 % complete ) and 6443 restraints for refining 2907 atoms. 5496 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3044 (Rfree = 0.000) for 2907 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 2: After refmac, R = 0.2672 (Rfree = 0.000) for 2869 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 3: After refmac, R = 0.2558 (Rfree = 0.000) for 2852 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 4: After refmac, R = 0.2450 (Rfree = 0.000) for 2844 atoms. Found 11 (15 requested) and removed 14 (7 requested) atoms. Cycle 5: After refmac, R = 0.2365 (Rfree = 0.000) for 2827 atoms. Found 7 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.58 3.26 Search for helices and strands: 0 residues in 0 chains, 2894 seeds are put forward NCS extension: 17 residues added (5 deleted due to clashes), 2911 seeds are put forward Round 1: 246 peptides, 37 chains. Longest chain 17 peptides. Score 0.494 Round 2: 268 peptides, 29 chains. Longest chain 24 peptides. Score 0.638 Round 3: 254 peptides, 28 chains. Longest chain 25 peptides. Score 0.617 Round 4: 271 peptides, 27 chains. Longest chain 24 peptides. Score 0.664 Round 5: 266 peptides, 32 chains. Longest chain 18 peptides. Score 0.602 Taking the results from Round 4 Chains 27, Residues 244, Estimated correctness of the model 26.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5456 reflections ( 99.67 % complete ) and 6486 restraints for refining 2908 atoms. 5537 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2885 (Rfree = 0.000) for 2908 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. Cycle 7: After refmac, R = 0.2589 (Rfree = 0.000) for 2895 atoms. Found 13 (15 requested) and removed 17 (7 requested) atoms. Cycle 8: After refmac, R = 0.2437 (Rfree = 0.000) for 2878 atoms. Found 15 (15 requested) and removed 21 (7 requested) atoms. Cycle 9: After refmac, R = 0.2086 (Rfree = 0.000) for 2867 atoms. Found 3 (15 requested) and removed 10 (7 requested) atoms. Cycle 10: After refmac, R = 0.2044 (Rfree = 0.000) for 2848 atoms. Found 6 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.51 3.20 Search for helices and strands: 0 residues in 0 chains, 2921 seeds are put forward NCS extension: 30 residues added (4 deleted due to clashes), 2951 seeds are put forward Round 1: 242 peptides, 32 chains. Longest chain 20 peptides. Score 0.543 Round 2: 240 peptides, 30 chains. Longest chain 16 peptides. Score 0.561 Round 3: 249 peptides, 30 chains. Longest chain 19 peptides. Score 0.583 Round 4: 272 peptides, 33 chains. Longest chain 16 peptides. Score 0.605 Round 5: 269 peptides, 31 chains. Longest chain 26 peptides. Score 0.619 Taking the results from Round 5 Chains 31, Residues 238, Estimated correctness of the model 7.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5456 reflections ( 99.67 % complete ) and 6417 restraints for refining 2909 atoms. 5496 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2562 (Rfree = 0.000) for 2909 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 12: After refmac, R = 0.2306 (Rfree = 0.000) for 2894 atoms. Found 8 (16 requested) and removed 14 (8 requested) atoms. Cycle 13: After refmac, R = 0.2208 (Rfree = 0.000) for 2877 atoms. Found 10 (15 requested) and removed 8 (7 requested) atoms. Cycle 14: After refmac, R = 0.2183 (Rfree = 0.000) for 2870 atoms. Found 9 (15 requested) and removed 12 (7 requested) atoms. Cycle 15: After refmac, R = 0.2079 (Rfree = 0.000) for 2861 atoms. Found 9 (15 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.55 3.23 Search for helices and strands: 0 residues in 0 chains, 2962 seeds are put forward NCS extension: 35 residues added (3 deleted due to clashes), 2997 seeds are put forward Round 1: 210 peptides, 31 chains. Longest chain 14 peptides. Score 0.466 Round 2: 231 peptides, 31 chains. Longest chain 14 peptides. Score 0.525 Round 3: 242 peptides, 30 chains. Longest chain 14 peptides. Score 0.566 Round 4: 245 peptides, 30 chains. Longest chain 16 peptides. Score 0.573 Round 5: 248 peptides, 30 chains. Longest chain 35 peptides. Score 0.581 Taking the results from Round 5 Chains 31, Residues 218, Estimated correctness of the model 0.0 % 1 chains (27 residues) have been docked in sequence ------------------------------------------------------ 5456 reflections ( 99.67 % complete ) and 6124 restraints for refining 2909 atoms. 5164 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2401 (Rfree = 0.000) for 2909 atoms. Found 12 (15 requested) and removed 10 (7 requested) atoms. Cycle 17: After refmac, R = 0.2229 (Rfree = 0.000) for 2890 atoms. Found 8 (16 requested) and removed 12 (8 requested) atoms. Cycle 18: After refmac, R = 0.2171 (Rfree = 0.000) for 2877 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 19: After refmac, R = 0.2077 (Rfree = 0.000) for 2872 atoms. Found 9 (15 requested) and removed 8 (7 requested) atoms. Cycle 20: After refmac, R = 0.2092 (Rfree = 0.000) for 2866 atoms. Found 12 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.51 3.20 Search for helices and strands: 0 residues in 0 chains, 2964 seeds are put forward NCS extension: 25 residues added (6 deleted due to clashes), 2989 seeds are put forward Round 1: 239 peptides, 35 chains. Longest chain 16 peptides. Score 0.499 Round 2: 246 peptides, 32 chains. Longest chain 15 peptides. Score 0.553 Round 3: 248 peptides, 28 chains. Longest chain 21 peptides. Score 0.603 Round 4: 240 peptides, 30 chains. Longest chain 16 peptides. Score 0.561 Round 5: 257 peptides, 27 chains. Longest chain 41 peptides. Score 0.634 Taking the results from Round 5 Chains 29, Residues 230, Estimated correctness of the model 14.1 % 1 chains (22 residues) have been docked in sequence ------------------------------------------------------ 5456 reflections ( 99.67 % complete ) and 6112 restraints for refining 2908 atoms. 5135 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2371 (Rfree = 0.000) for 2908 atoms. Found 13 (15 requested) and removed 13 (7 requested) atoms. Cycle 22: After refmac, R = 0.2241 (Rfree = 0.000) for 2886 atoms. Found 9 (15 requested) and removed 12 (7 requested) atoms. Cycle 23: After refmac, R = 0.2229 (Rfree = 0.000) for 2873 atoms. Found 13 (15 requested) and removed 9 (7 requested) atoms. Cycle 24: After refmac, R = 0.2141 (Rfree = 0.000) for 2869 atoms. Found 9 (15 requested) and removed 10 (7 requested) atoms. Cycle 25: After refmac, R = 0.2086 (Rfree = 0.000) for 2865 atoms. Found 12 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.47 3.16 Search for helices and strands: 0 residues in 0 chains, 2957 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 2976 seeds are put forward Round 1: 221 peptides, 36 chains. Longest chain 15 peptides. Score 0.434 Round 2: 239 peptides, 30 chains. Longest chain 24 peptides. Score 0.558 Round 3: 236 peptides, 32 chains. Longest chain 22 peptides. Score 0.527 Round 4: 231 peptides, 33 chains. Longest chain 16 peptides. Score 0.501 Round 5: 234 peptides, 32 chains. Longest chain 17 peptides. Score 0.521 Taking the results from Round 2 Chains 30, Residues 209, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 5456 reflections ( 99.67 % complete ) and 6300 restraints for refining 2908 atoms. 5439 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2344 (Rfree = 0.000) for 2908 atoms. Found 14 (15 requested) and removed 8 (7 requested) atoms. Cycle 27: After refmac, R = 0.2205 (Rfree = 0.000) for 2901 atoms. Found 15 (16 requested) and removed 12 (8 requested) atoms. Cycle 28: After refmac, R = 0.2198 (Rfree = 0.000) for 2901 atoms. Found 12 (15 requested) and removed 12 (7 requested) atoms. Cycle 29: After refmac, R = 0.2043 (Rfree = 0.000) for 2894 atoms. Found 9 (15 requested) and removed 9 (7 requested) atoms. Cycle 30: After refmac, R = 0.2141 (Rfree = 0.000) for 2887 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.52 3.20 Search for helices and strands: 0 residues in 0 chains, 2968 seeds are put forward NCS extension: 33 residues added (2 deleted due to clashes), 3001 seeds are put forward Round 1: 210 peptides, 36 chains. Longest chain 13 peptides. Score 0.400 Round 2: 207 peptides, 28 chains. Longest chain 22 peptides. Score 0.496 Round 3: 231 peptides, 29 chains. Longest chain 22 peptides. Score 0.549 Round 4: 228 peptides, 28 chains. Longest chain 15 peptides. Score 0.553 Round 5: 231 peptides, 33 chains. Longest chain 20 peptides. Score 0.501 Taking the results from Round 4 Chains 29, Residues 200, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5456 reflections ( 99.67 % complete ) and 6402 restraints for refining 2906 atoms. 5603 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2302 (Rfree = 0.000) for 2906 atoms. Found 8 (15 requested) and removed 13 (7 requested) atoms. Cycle 32: After refmac, R = 0.2128 (Rfree = 0.000) for 2883 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 33: After refmac, R = 0.2206 (Rfree = 0.000) for 2877 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 34: After refmac, R = 0.2002 (Rfree = 0.000) for 2872 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 35: After refmac, R = 0.1719 (Rfree = 0.000) for 2872 atoms. Found 1 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.51 3.20 Search for helices and strands: 0 residues in 0 chains, 2971 seeds are put forward NCS extension: 0 residues added, 2971 seeds are put forward Round 1: 202 peptides, 38 chains. Longest chain 10 peptides. Score 0.346 Round 2: 220 peptides, 34 chains. Longest chain 16 peptides. Score 0.457 Round 3: 222 peptides, 33 chains. Longest chain 16 peptides. Score 0.475 Round 4: 222 peptides, 34 chains. Longest chain 18 peptides. Score 0.463 Round 5: 229 peptides, 33 chains. Longest chain 15 peptides. Score 0.495 Taking the results from Round 5 Chains 33, Residues 196, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5456 reflections ( 99.67 % complete ) and 6596 restraints for refining 2908 atoms. 5845 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2088 (Rfree = 0.000) for 2908 atoms. Found 12 (15 requested) and removed 9 (7 requested) atoms. Cycle 37: After refmac, R = 0.2120 (Rfree = 0.000) for 2895 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 38: After refmac, R = 0.1961 (Rfree = 0.000) for 2885 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 39: After refmac, R = 0.1976 (Rfree = 0.000) for 2886 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 40: After refmac, R = 0.1837 (Rfree = 0.000) for 2890 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.51 3.20 Search for helices and strands: 0 residues in 0 chains, 2978 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 2996 seeds are put forward Round 1: 187 peptides, 36 chains. Longest chain 12 peptides. Score 0.324 Round 2: 209 peptides, 32 chains. Longest chain 18 peptides. Score 0.450 Round 3: 195 peptides, 31 chains. Longest chain 18 peptides. Score 0.421 Round 4: 206 peptides, 32 chains. Longest chain 15 peptides. Score 0.441 Round 5: 203 peptides, 31 chains. Longest chain 13 peptides. Score 0.445 Taking the results from Round 2 Chains 33, Residues 177, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 5456 reflections ( 99.67 % complete ) and 6593 restraints for refining 2909 atoms. 5862 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2173 (Rfree = 0.000) for 2909 atoms. Found 10 (15 requested) and removed 10 (7 requested) atoms. Cycle 42: After refmac, R = 0.2159 (Rfree = 0.000) for 2893 atoms. Found 10 (15 requested) and removed 7 (7 requested) atoms. Cycle 43: After refmac, R = 0.2294 (Rfree = 0.000) for 2886 atoms. Found 15 (15 requested) and removed 7 (7 requested) atoms. Cycle 44: After refmac, R = 0.2093 (Rfree = 0.000) for 2887 atoms. Found 13 (15 requested) and removed 8 (7 requested) atoms. Cycle 45: After refmac, R = 0.2157 (Rfree = 0.000) for 2882 atoms. Found 15 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.48 3.17 Search for helices and strands: 0 residues in 0 chains, 2976 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 3000 seeds are put forward Round 1: 176 peptides, 36 chains. Longest chain 8 peptides. Score 0.286 Round 2: 199 peptides, 35 chains. Longest chain 12 peptides. Score 0.378 Round 3: 200 peptides, 35 chains. Longest chain 14 peptides. Score 0.382 Round 4: 202 peptides, 35 chains. Longest chain 12 peptides. Score 0.388 Round 5: 201 peptides, 32 chains. Longest chain 14 peptides. Score 0.426 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 169, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 2p97-3_warpNtrace.pdb as input Building loops using Loopy2018 33 chains (169 residues) following loop building 3 chains (17 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5456 reflections ( 99.67 % complete ) and 6543 restraints for refining 2908 atoms. 5849 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2330 (Rfree = 0.000) for 2908 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2265 (Rfree = 0.000) for 2876 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2119 (Rfree = 0.000) for 2864 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2121 (Rfree = 0.000) for 2852 atoms. TimeTaking 34.48