null Mon 24 Dec 07:47:45 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 2pr7-1.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2pr7-1.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2pr7-1.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pr7-1.4-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/2pr7-1.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pr7-1.4-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 07:47:49 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/2pr7-1.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pr7-1.4-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 288 and 0 Target number of residues in the AU: 288 Target solvent content: 0.4668 Checking the provided sequence file Detected sequence length: 137 Maximum limit of NCS related copies: 16 Number of NCS-related molecules: 2 Adjusted target number of residues: 274 Adjusted target solvent content: 0.49 Input MTZ file: 2pr7-1.4-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: 1 Cell parameters: 29.149 45.153 60.777 100.722 103.858 103.308 Input sequence file: 2pr7-1.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 2192 target number of atoms Had to go as low as 0.45 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 1 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 Loops will be built when appropriate and at the last cycle Resolution range: 57.053 1.440 Wilson plot Bfac: 17.25 40620 reflections ( 79.26 % complete ) and 0 restraints for refining 2430 atoms. Observations/parameters ratio is 4.18 ------------------------------------------------------ Starting model: R = 0.3329 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2785 (Rfree = 0.000) for 2430 atoms. Found 135 (212 requested) and removed 112 (106 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.71 1.73 Round 1: 238 peptides, 14 chains. Longest chain 43 peptides. Score 0.875 Round 2: 261 peptides, 8 chains. Longest chain 63 peptides. Score 0.935 Round 3: 267 peptides, 5 chains. Longest chain 73 peptides. Score 0.953 Round 4: 260 peptides, 7 chains. Longest chain 67 peptides. Score 0.939 Round 5: 261 peptides, 8 chains. Longest chain 63 peptides. Score 0.935 Taking the results from Round 3 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 40620 reflections ( 79.26 % complete ) and 2322 restraints for refining 2300 atoms. 352 conditional restraints added. Observations/parameters ratio is 4.42 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2865 (Rfree = 0.000) for 2300 atoms. Found 117 (200 requested) and removed 37 (100 requested) atoms. Cycle 2: After refmac, R = 0.2696 (Rfree = 0.000) for 2377 atoms. Found 86 (207 requested) and removed 9 (103 requested) atoms. Cycle 3: After refmac, R = 0.2457 (Rfree = 0.000) for 2452 atoms. Found 61 (214 requested) and removed 9 (107 requested) atoms. Cycle 4: After refmac, R = 0.2322 (Rfree = 0.000) for 2490 atoms. Found 66 (218 requested) and removed 7 (109 requested) atoms. Cycle 5: After refmac, R = 0.2218 (Rfree = 0.000) for 2539 atoms. Found 44 (222 requested) and removed 5 (111 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.67 1.69 Round 1: 268 peptides, 4 chains. Longest chain 74 peptides. Score 0.958 Round 2: 268 peptides, 4 chains. Longest chain 74 peptides. Score 0.958 Round 3: 266 peptides, 6 chains. Longest chain 63 peptides. Score 0.948 Round 4: 268 peptides, 4 chains. Longest chain 74 peptides. Score 0.958 Round 5: 267 peptides, 5 chains. Longest chain 74 peptides. Score 0.953 Taking the results from Round 4 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 40620 reflections ( 79.26 % complete ) and 2449 restraints for refining 2442 atoms. 462 conditional restraints added. Observations/parameters ratio is 4.16 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2269 (Rfree = 0.000) for 2442 atoms. Found 91 (213 requested) and removed 17 (106 requested) atoms. Cycle 7: After refmac, R = 0.2170 (Rfree = 0.000) for 2511 atoms. Found 63 (219 requested) and removed 4 (109 requested) atoms. Cycle 8: After refmac, R = 0.2089 (Rfree = 0.000) for 2564 atoms. Found 61 (224 requested) and removed 8 (112 requested) atoms. Cycle 9: After refmac, R = 0.2029 (Rfree = 0.000) for 2616 atoms. Found 57 (228 requested) and removed 15 (114 requested) atoms. Cycle 10: After refmac, R = 0.1989 (Rfree = 0.000) for 2652 atoms. Found 61 (232 requested) and removed 10 (116 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.67 1.69 Round 1: 269 peptides, 4 chains. Longest chain 74 peptides. Score 0.959 Round 2: 269 peptides, 4 chains. Longest chain 74 peptides. Score 0.959 Round 3: 269 peptides, 5 chains. Longest chain 74 peptides. Score 0.954 Round 4: 268 peptides, 6 chains. Longest chain 74 peptides. Score 0.949 Round 5: 271 peptides, 4 chains. Longest chain 137 peptides. Score 0.959 Taking the results from Round 5 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 40620 reflections ( 79.26 % complete ) and 2532 restraints for refining 2539 atoms. 522 conditional restraints added. Observations/parameters ratio is 4.00 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2164 (Rfree = 0.000) for 2539 atoms. Found 109 (221 requested) and removed 16 (110 requested) atoms. Cycle 12: After refmac, R = 0.2088 (Rfree = 0.000) for 2630 atoms. Found 69 (229 requested) and removed 5 (114 requested) atoms. Cycle 13: After refmac, R = 0.2014 (Rfree = 0.000) for 2688 atoms. Found 64 (235 requested) and removed 2 (117 requested) atoms. Cycle 14: After refmac, R = 0.1978 (Rfree = 0.000) for 2748 atoms. Found 62 (240 requested) and removed 14 (120 requested) atoms. Cycle 15: After refmac, R = 0.1932 (Rfree = 0.000) for 2788 atoms. Found 76 (244 requested) and removed 14 (122 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.68 1.70 Round 1: 269 peptides, 4 chains. Longest chain 74 peptides. Score 0.959 Round 2: 268 peptides, 5 chains. Longest chain 74 peptides. Score 0.954 Round 3: 269 peptides, 5 chains. Longest chain 74 peptides. Score 0.954 Round 4: 269 peptides, 5 chains. Longest chain 74 peptides. Score 0.954 Round 5: 267 peptides, 5 chains. Longest chain 108 peptides. Score 0.953 Taking the results from Round 1 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 40620 reflections ( 79.26 % complete ) and 2664 restraints for refining 2631 atoms. 669 conditional restraints added. Observations/parameters ratio is 3.86 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2108 (Rfree = 0.000) for 2631 atoms. Found 118 (229 requested) and removed 14 (114 requested) atoms. Cycle 17: After refmac, R = 0.2049 (Rfree = 0.000) for 2734 atoms. Found 59 (238 requested) and removed 13 (119 requested) atoms. Cycle 18: After refmac, R = 0.1992 (Rfree = 0.000) for 2777 atoms. Found 45 (242 requested) and removed 15 (121 requested) atoms. Cycle 19: After refmac, R = 0.1942 (Rfree = 0.000) for 2804 atoms. Found 48 (245 requested) and removed 13 (122 requested) atoms. Cycle 20: After refmac, R = 0.1923 (Rfree = 0.000) for 2829 atoms. Found 60 (248 requested) and removed 17 (124 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.67 1.69 Round 1: 267 peptides, 4 chains. Longest chain 74 peptides. Score 0.958 Round 2: 266 peptides, 5 chains. Longest chain 74 peptides. Score 0.953 Round 3: 266 peptides, 6 chains. Longest chain 62 peptides. Score 0.948 Round 4: 267 peptides, 6 chains. Longest chain 62 peptides. Score 0.949 Round 5: 269 peptides, 3 chains. Longest chain 136 peptides. Score 0.963 Taking the results from Round 5 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 40620 reflections ( 79.26 % complete ) and 2668 restraints for refining 2636 atoms. 667 conditional restraints added. Observations/parameters ratio is 3.85 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2141 (Rfree = 0.000) for 2636 atoms. Found 121 (230 requested) and removed 19 (115 requested) atoms. Cycle 22: After refmac, R = 0.2056 (Rfree = 0.000) for 2734 atoms. Found 79 (239 requested) and removed 7 (119 requested) atoms. Cycle 23: After refmac, R = 0.2003 (Rfree = 0.000) for 2802 atoms. Found 54 (245 requested) and removed 11 (122 requested) atoms. Cycle 24: After refmac, R = 0.1939 (Rfree = 0.000) for 2840 atoms. Found 63 (248 requested) and removed 15 (124 requested) atoms. Cycle 25: After refmac, R = 0.1919 (Rfree = 0.000) for 2880 atoms. Found 74 (252 requested) and removed 19 (126 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.68 1.70 Round 1: 267 peptides, 4 chains. Longest chain 74 peptides. Score 0.958 Round 2: 268 peptides, 4 chains. Longest chain 136 peptides. Score 0.958 Round 3: 264 peptides, 6 chains. Longest chain 62 peptides. Score 0.947 Round 4: 265 peptides, 6 chains. Longest chain 72 peptides. Score 0.947 Round 5: 266 peptides, 4 chains. Longest chain 73 peptides. Score 0.957 Taking the results from Round 2 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 40620 reflections ( 79.26 % complete ) and 2748 restraints for refining 2706 atoms. 759 conditional restraints added. Observations/parameters ratio is 3.75 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2108 (Rfree = 0.000) for 2706 atoms. Found 133 (236 requested) and removed 19 (118 requested) atoms. Cycle 27: After refmac, R = 0.2042 (Rfree = 0.000) for 2816 atoms. Found 61 (246 requested) and removed 8 (123 requested) atoms. Cycle 28: After refmac, R = 0.1962 (Rfree = 0.000) for 2860 atoms. Found 53 (250 requested) and removed 11 (125 requested) atoms. Cycle 29: After refmac, R = 0.1916 (Rfree = 0.000) for 2897 atoms. Found 42 (253 requested) and removed 18 (126 requested) atoms. Cycle 30: After refmac, R = 0.1884 (Rfree = 0.000) for 2911 atoms. Found 59 (255 requested) and removed 14 (127 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.67 1.69 Round 1: 267 peptides, 4 chains. Longest chain 74 peptides. Score 0.958 Round 2: 266 peptides, 5 chains. Longest chain 74 peptides. Score 0.953 Round 3: 266 peptides, 6 chains. Longest chain 62 peptides. Score 0.948 Round 4: 265 peptides, 6 chains. Longest chain 74 peptides. Score 0.947 Round 5: 266 peptides, 5 chains. Longest chain 74 peptides. Score 0.953 Taking the results from Round 1 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 40620 reflections ( 79.26 % complete ) and 2839 restraints for refining 2727 atoms. 865 conditional restraints added. Observations/parameters ratio is 3.72 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2085 (Rfree = 0.000) for 2727 atoms. Found 141 (238 requested) and removed 12 (119 requested) atoms. Cycle 32: After refmac, R = 0.2029 (Rfree = 0.000) for 2853 atoms. Found 71 (249 requested) and removed 15 (124 requested) atoms. Cycle 33: After refmac, R = 0.1969 (Rfree = 0.000) for 2903 atoms. Found 67 (254 requested) and removed 13 (127 requested) atoms. Cycle 34: After refmac, R = 0.1934 (Rfree = 0.000) for 2951 atoms. Found 47 (258 requested) and removed 24 (129 requested) atoms. Cycle 35: After refmac, R = 0.1894 (Rfree = 0.000) for 2970 atoms. Found 51 (254 requested) and removed 10 (129 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.67 1.69 Round 1: 267 peptides, 4 chains. Longest chain 74 peptides. Score 0.958 Round 2: 267 peptides, 4 chains. Longest chain 74 peptides. Score 0.958 Round 3: 264 peptides, 6 chains. Longest chain 62 peptides. Score 0.947 Round 4: 263 peptides, 6 chains. Longest chain 62 peptides. Score 0.946 Round 5: 264 peptides, 6 chains. Longest chain 63 peptides. Score 0.947 Taking the results from Round 2 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 40620 reflections ( 79.26 % complete ) and 2860 restraints for refining 2764 atoms. 886 conditional restraints added. Observations/parameters ratio is 3.67 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2082 (Rfree = 0.000) for 2764 atoms. Found 129 (236 requested) and removed 13 (120 requested) atoms. Cycle 37: After refmac, R = 0.2027 (Rfree = 0.000) for 2877 atoms. Found 70 (246 requested) and removed 14 (125 requested) atoms. Cycle 38: After refmac, R = 0.1954 (Rfree = 0.000) for 2927 atoms. Found 60 (251 requested) and removed 9 (128 requested) atoms. Cycle 39: After refmac, R = 0.1925 (Rfree = 0.000) for 2972 atoms. Found 51 (255 requested) and removed 15 (130 requested) atoms. Cycle 40: After refmac, R = 0.1887 (Rfree = 0.000) for 3000 atoms. Found 68 (257 requested) and removed 21 (131 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.66 1.68 Round 1: 267 peptides, 4 chains. Longest chain 74 peptides. Score 0.958 Round 2: 265 peptides, 5 chains. Longest chain 74 peptides. Score 0.952 Round 3: 266 peptides, 5 chains. Longest chain 74 peptides. Score 0.953 Round 4: 264 peptides, 5 chains. Longest chain 74 peptides. Score 0.951 Round 5: 265 peptides, 5 chains. Longest chain 74 peptides. Score 0.952 Taking the results from Round 1 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 40620 reflections ( 79.26 % complete ) and 2927 restraints for refining 2784 atoms. 953 conditional restraints added. Observations/parameters ratio is 3.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2074 (Rfree = 0.000) for 2784 atoms. Found 137 (238 requested) and removed 12 (121 requested) atoms. Cycle 42: After refmac, R = 0.2028 (Rfree = 0.000) for 2906 atoms. Found 63 (249 requested) and removed 15 (127 requested) atoms. Cycle 43: After refmac, R = 0.1967 (Rfree = 0.000) for 2945 atoms. Found 66 (253 requested) and removed 11 (129 requested) atoms. Cycle 44: After refmac, R = 0.1936 (Rfree = 0.000) for 2993 atoms. Found 59 (257 requested) and removed 24 (131 requested) atoms. Cycle 45: After refmac, R = 0.1896 (Rfree = 0.000) for 3019 atoms. Found 67 (259 requested) and removed 15 (132 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.67 1.69 Round 1: 266 peptides, 4 chains. Longest chain 74 peptides. Score 0.957 Round 2: 266 peptides, 4 chains. Longest chain 74 peptides. Score 0.957 Round 3: 263 peptides, 6 chains. Longest chain 62 peptides. Score 0.946 Round 4: 264 peptides, 6 chains. Longest chain 62 peptides. Score 0.947 Round 5: 264 peptides, 5 chains. Longest chain 74 peptides. Score 0.951 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2pr7-1_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 40620 reflections ( 79.26 % complete ) and 3008 restraints for refining 2800 atoms. 1042 conditional restraints added. Observations/parameters ratio is 3.63 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2097 (Rfree = 0.000) for 2800 atoms. Found 0 (239 requested) and removed 6 (122 requested) atoms. Cycle 47: After refmac, R = 0.2003 (Rfree = 0.000) for 2789 atoms. Found 0 (234 requested) and removed 1 (122 requested) atoms. Cycle 48: After refmac, R = 0.1952 (Rfree = 0.000) for 2783 atoms. Found 0 (228 requested) and removed 0 (121 requested) atoms. Cycle 49: After refmac, R = 0.1920 (Rfree = 0.000) for 2777 atoms. Found 0 (228 requested) and removed 0 (121 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:19:04 GMT 2018 Job finished. TimeTaking 31.31 Used memory is bytes: 7057568